Full wwPDB NMR Structure Validation Report i○

Feb 17, 2018 – 07:11 pm GMT

PDB ID : 2K6OTitle : Human LL-37 Structure

Authors : Wang, G.Deposited on : 2008-07-14

This is a Full wwPDB NMR Structure Validation Report for a publicly released PDB entry.

We welcome your comments at validation@mail.wwpdb.orgA user guide is available at

https://www.wwpdb.org/validation/2017/NMRValidationReportHelpwith specific help available everywhere you see the i○ symbol.

The following versions of software and data (see references i○) were used in the production of this report:

Cyrange : Kirchner and Güntert (2011)NmrClust : Kelley et al. (1996)

MolProbity : 4.02b-467Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017)

RCI : v_1n_11_5_13_A (Berjanski et al., 2005)PANAV : Wang et al. (2010)

ShiftChecker : trunk30686Ideal geometry (proteins) : Engh & Huber (2001)

Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : trunk30686

Page 2 Full wwPDB NMR Structure Validation Report 2K6O

1 Overall quality at a glance i○

The following experimental techniques were used to determine the structure:SOLUTION NMR

The overall completeness of chemical shifts assignment is 33%.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

Metric Whole archive(#Entries)

NMR archive(#Entries)

Clashscore 136279 12091Ramachandran outliers 132675 10835

Sidechain outliers 132484 10811

The table below summarises the geometric issues observed across the polymeric chains and theirfit to the experimental data. The red, orange, yellow and green segments indicate the fractionof residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A cyansegment indicates the fraction of residues that are not part of the well-defined cores, and a grey seg-ment represents the fraction of residues that are not modelled. The numeric value for each fractionis indicated below the corresponding segment, with a dot representing fractions <=5%

Mol Chain Length Quality of chain

1 A 37

Page 3 Full wwPDB NMR Structure Validation Report 2K6O

2 Ensemble composition and analysis i○

This entry contains 4 models. Model 4 is the overall representative, medoid model (most similarto other models). The authors have identified model 1 as representative, based on the followingcriterion: closest to the average.

The following residues are included in the computation of the global validation metrics.

Well-defined (core) protein residuesWell-defined core Residue range (total) Backbone RMSD (Å) Medoid model

1 A:2-A:31 (30) 0.53 4

Ill-defined regions of proteins are excluded from the global statistics.

Ligands and non-protein polymers are included in the analysis.

The models can be grouped into 1 clusters. No single-model clusters were found.

Cluster number Models1 1, 2, 3, 4

Page 4 Full wwPDB NMR Structure Validation Report 2K6O

3 Entry composition i○

There is only 1 type of molecule in this entry. The entry contains 664 atoms, of which 346 arehydrogens and 0 are deuteriums.

• Molecule 1 is a protein called Cathelicidin antimicrobial peptide.

Mol Chain Residues Atoms Trace

1 A 37 Total C H N O664 205 346 60 53 0

Page 5 Full wwPDB NMR Structure Validation Report 2K6O

4 Residue-property plots i○

4.1 Average score per residue in the NMR ensemble

These plots are provided for all protein, RNA and DNA chains in the entry. The first graphic is thesame as shown in the summary in section 1 of this report. The second graphic shows the sequencewhere residues are colour-coded according to the number of geometric quality criteria for whichthey contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretchesof 2 or more consecutive residues without any outliers are shown as green connectors. Residueswhich are classified as ill-defined in the NMR ensemble, are shown in cyan with an underlinecolour-coded according to the previous scheme. Residues which were present in the experimentalsample, but not modelled in the final structure are shown in grey.

• Molecule 1: Cathelicidin antimicrobial peptide

Chain A:

L1 L2 R7 K8 S9 K12

I13

G14

K15

E16

F17

K18

R19

Q22

R23

I24

K25

D26

F27

L28

R29

N30

L31

V32

P33

R34

T35

E36

S37

4.2 Scores per residue for each member of the ensemble

Colouring as in section 4.1 above.

4.2.1 Score per residue for model 1

• Molecule 1: Cathelicidin antimicrobial peptide

Chain A:

L1 L2 F6 S9 I13

G14

F17

F27

L31

V32

P33

R34

T35

E36

S37

4.2.2 Score per residue for model 2

• Molecule 1: Cathelicidin antimicrobial peptide

Chain A:

L1 L2 R7 K12

I13

G14

K15

E16

F17

Q22

R23

I24

F27

L28

L31

V32

P33

R34

T35

E36

S37

Page 6 Full wwPDB NMR Structure Validation Report 2K6O

4.2.3 Score per residue for model 3

• Molecule 1: Cathelicidin antimicrobial peptide

Chain A:

L1 L2 K10

I13

G14

K15

E16

F17

I20

V21

D26

F27

L28

R29

N30

L31

V32

P33

R34

T35

E36

S37

4.2.4 Score per residue for model 4 (medoid)

• Molecule 1: Cathelicidin antimicrobial peptide

Chain A:

L1 L2 S9 K12

I13

G14

F17

K18

R19

R23

I24

K25

D26

F27

L28

R29

N30

L31

V32

P33

R34

T35

E36

S37

Page 7 Full wwPDB NMR Structure Validation Report 2K6O

5 Refinement protocol and experimental data overview i○

The models were refined using the following method: simulated annealing.

Of the 200 calculated structures, 4 were deposited, based on the following criterion: structureswith the lowest energy.

The following table shows the software used for structure solution, optimisation and refinement.

Software name Classification VersionX-PLOR NIH refinement

The following table shows chemical shift validation statistics as aggregates over all chemical shiftfiles. Detailed validation can be found in section 7 of this report.

Chemical shift file(s) BMRB entry 15876Number of chemical shift lists 1Total number of shifts 179Number of shifts mapped to atoms 179Number of unparsed shifts 0Number of shifts with mapping errors 0Number of shifts with mapping warnings 0Assignment completeness (well-defined parts) 33%

No validations of the models with respect to experimental NMR restraints is performed at thistime.

Page 8 Full wwPDB NMR Structure Validation Report 2K6O

6 Model quality i○

6.1 Standard geometry i○

There are no covalent bond-length or bond-angle outliers.

There are no bond-length outliers.

There are no bond-angle outliers.

There are no chirality outliers.

There are no planarity outliers.

6.2 Too-close contacts i○

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in each chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashesaveraged over the ensemble.

Mol Chain Non-H H(model) H(added) Clashes1 A 262 286 286 14±6All All 1048 1144 1144 54

The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 25.

All unique clashes are listed below, sorted by their clash magnitude.

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:28:LEU:H 1:A:28:LEU:HD22 0.90 1.23 2 11:A:28:LEU:H 1:A:28:LEU:CD2 0.67 2.00 2 1

1:A:27:PHE:CE2 1:A:31:LEU:HD13 0.66 2.26 1 11:A:28:LEU:N 1:A:28:LEU:HD22 0.66 2.02 2 11:A:7:ARG:CG 1:A:7:ARG:HH11 0.60 2.10 2 11:A:23:ARG:CG 1:A:23:ARG:HH11 0.60 2.09 4 21:A:19:ARG:HH11 1:A:19:ARG:CG 0.59 2.11 4 11:A:23:ARG:CG 1:A:23:ARG:NH1 0.59 2.66 4 21:A:13:ILE:CG1 1:A:14:GLY:N 0.58 2.67 1 31:A:13:ILE:O 1:A:17:PHE:N 0.57 2.33 4 3

1:A:19:ARG:NH1 1:A:19:ARG:CG 0.57 2.67 4 11:A:27:PHE:O 1:A:31:LEU:N 0.56 2.38 3 21:A:7:ARG:CG 1:A:7:ARG:NH1 0.56 2.66 2 11:A:26:ASP:O 1:A:30:ASN:ND2 0.54 2.41 4 1

Continued on next page...

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Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:16:GLU:N 1:A:16:GLU:OE1 0.53 2.42 2 11:A:27:PHE:CZ 1:A:31:LEU:HD13 0.52 2.39 1 11:A:24:ILE:O 1:A:28:LEU:HD22 0.52 2.05 2 1

1:A:2:LEU:HD13 1:A:2:LEU:O 0.52 2.05 2 21:A:2:LEU:O 1:A:2:LEU:HD13 0.51 2.05 1 2

1:A:29:ARG:CZ 1:A:29:ARG:CB 0.50 2.88 4 11:A:29:ARG:HG3 1:A:29:ARG:HH11 0.50 1.67 4 11:A:26:ASP:OD2 1:A:30:ASN:ND2 0.49 2.45 3 11:A:24:ILE:O 1:A:28:LEU:CD2 0.49 2.60 2 1

1:A:29:ARG:CG 1:A:29:ARG:NH1 0.48 2.75 4 11:A:13:ILE:O 1:A:17:PHE:CB 0.48 2.62 2 11:A:28:LEU:N 1:A:28:LEU:HD12 0.48 2.24 4 11:A:29:ARG:CG 1:A:29:ARG:HH11 0.47 2.22 4 11:A:7:ARG:HG2 1:A:7:ARG:HH11 0.47 1.70 2 11:A:27:PHE:CZ 1:A:31:LEU:HD11 0.47 2.44 4 11:A:27:PHE:CE2 1:A:31:LEU:HD11 0.46 2.44 3 11:A:9:SER:O 1:A:13:ILE:HG23 0.46 2.09 1 2

1:A:2:LEU:HD12 1:A:6:PHE:CE2 0.46 2.46 1 11:A:23:ARG:HG2 1:A:23:ARG:HH11 0.45 1.72 2 21:A:17:PHE:O 1:A:20:ILE:CG1 0.45 2.64 3 11:A:12:LYS:O 1:A:16:GLU:OE2 0.44 2.36 2 1

1:A:13:ILE:HG13 1:A:14:GLY:N 0.43 2.28 2 11:A:20:ILE:HG13 1:A:21:VAL:N 0.43 2.28 3 11:A:22:GLN:O 1:A:22:GLN:OE1 0.43 2.37 2 11:A:2:LEU:CD1 1:A:6:PHE:CE2 0.43 3.01 1 11:A:24:ILE:O 1:A:27:PHE:N 0.42 2.52 2 11:A:16:GLU:N 1:A:16:GLU:CD 0.42 2.72 2 11:A:28:LEU:HA 1:A:31:LEU:HD12 0.41 1.91 3 11:A:30:ASN:N 1:A:30:ASN:HD22 0.41 2.14 4 1

6.3 Torsion angles i○

6.3.1 Protein backbone i○

In the following table, the Percentiles column shows the percent Ramachandran outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the backbone conformationwas analysed and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 30/37 (81%) 30±0 (99±1%) 0±0 (1±1%) 0±0 (0±0%) 100 100Continued on next page...

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Continued from previous page...Mol Chain Analysed Favoured Allowed Outliers Percentiles

All All 120/148 (81%) 119 (99%) 1 (1%) 0 (0%) 100 100

There are no Ramachandran outliers.

6.3.2 Protein sidechains i○

In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the sidechain conformationwas analysed and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 28/35 (80%) 23±2 (82±8%) 5±2 (18±8%) 5 39

All All 112/140 (80%) 92 (82%) 20 (18%) 5 39

All 14 unique residues with a non-rotameric sidechain are listed below. They are sorted by thefrequency of occurrence in the ensemble.

Mol Chain Res Type Models (Total)1 A 2 LEU 41 A 13 ILE 31 A 23 ARG 21 A 25 LYS 11 A 12 LYS 11 A 31 LEU 11 A 24 ILE 11 A 19 ARG 11 A 7 ARG 11 A 29 ARG 11 A 15 LYS 11 A 10 LYS 11 A 22 GLN 11 A 16 GLU 1

6.3.3 RNA i○

There are no RNA molecules in this entry.

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6.4 Non-standard residues in protein, DNA, RNA chains i○

There are no non-standard protein/DNA/RNA residues in this entry.

6.5 Carbohydrates i○

There are no carbohydrates in this entry.

6.6 Ligand geometry i○

There are no ligands in this entry.

6.7 Other polymers i○

There are no such molecules in this entry.

6.8 Polymer linkage issues i○

There are no chain breaks in this entry.

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7 Chemical shift validation i○

The completeness of assignment taking into account all chemical shift lists is 33% for the well-defined parts and 33% for the entire structure.

7.1 Chemical shift list 1

File name: BMRB entry 15876

Chemical shift list name: assigned_chem_shift_list_1

7.1.1 Bookkeeping i○

The following table shows the results of parsing the chemical shift list and reports the number ofnuclei with statistically unusual chemical shifts.

Total number of shifts 179Number of shifts mapped to atoms 179Number of unparsed shifts 0Number of shifts with mapping errors 0Number of shifts with mapping warnings 0Number of shift outliers (ShiftChecker) 0

7.1.2 Chemical shift referencing i○

The following table shows the suggested chemical shift referencing corrections.

Nucleus # values Correction ± precision, ppm Suggested action13Cα 37 -0.69 ± 0.25 Should be applied13Cβ 35 0.15 ± 0.10 None needed (< 0.5 ppm)13C′ 34 -0.28 ± 0.17 None needed (< 0.5 ppm)15N 36 0.55 ± 0.41 None needed (imprecise)

7.1.3 Completeness of resonance assignments i○

The following table shows the completeness of the chemical shift assignments for the well-definedregions of the structure. The overall completeness is 33%, i.e. 148 atoms were assigned a chemicalshift out of a possible 450. 0 out of 4 assigned methyl groups (LEU and VAL) were assignedstereospecifically.

Total 1H 13C 15NBackbone 120/150 (80%) 30/60 (50%) 60/60 (100%) 30/30 (100%)Sidechain 28/264 (11%) 0/157 (0%) 28/87 (32%) 0/20 (0%)

Continued on next page...

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Continued from previous page...Total 1H 13C 15N

Aromatic 0/36 (0%) 0/20 (0%) 0/16 (0%) 0/0 (—%)Overall 148/450 (33%) 30/237 (13%) 88/163 (54%) 30/50 (60%)

The following table shows the completeness of the chemical shift assignments for the full structure.The overall completeness is 33%, i.e. 177 atoms were assigned a chemical shift out of a possible539. 0 out of 6 assigned methyl groups (LEU and VAL) were assigned stereospecifically.

Total 1H 13C 15NBackbone 142/183 (78%) 35/73 (48%) 71/74 (96%) 36/36 (100%)Sidechain 35/320 (11%) 0/190 (0%) 35/107 (33%) 0/23 (0%)Aromatic 0/36 (0%) 0/20 (0%) 0/16 (0%) 0/0 (—%)Overall 177/539 (33%) 35/283 (12%) 106/197 (54%) 36/59 (61%)

7.1.4 Statistically unusual chemical shifts i○

There are no statistically unusual chemical shifts.

7.1.5 Random Coil Index (RCI) plots i○

The image below reports random coil index values for the protein chains in the structure. Theheight of each bar gives a probability of a given residue to be disordered, as predicted fromthe available chemical shifts and the amino acid sequence. A value above 0.2 is an indicationof significant predicted disorder. The colour of the bar shows whether the residue is in the well-defined core (black) or in the ill-defined residue ranges (cyan), as described in section 2 on ensemblecomposition.

Random coil index (RCI) for chain A: