SMTL ID : 6cpn.1

Crystal structure of DR11 presenting the RQ13 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: V.116, N.118, E.166, H.167, W.168 Chain B: D.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.2, B:D.2

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: S.77, N.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.78 NAG.9: 2 residues within 4Å: Chain B: N.19, E.22 No protein-ligand interaction detected (PLIP)

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: P.96, V.97, D.181 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.97, A:D.181 SO4.4: 4 residues within 4Å: Chain A: R.123, N.124, K.126, D.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.124 Salt bridges: A:R.123, A:K.126 SO4.5: 5 residues within 4Å: Chain A: T.41, W.43, A.52, S.53, F.54 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.41, A:A.52, A:F.54 Water bridges: A:T.41, A:T.41 SO4.6: 1 residues within 4Å: Chain A: I.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.1, A:I.1 SO4.8: 3 residues within 4Å: Chain A: D.110, K.111, R.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.110 Salt bridges: A:K.111, A:R.140 SO4.10: 4 residues within 4Å: Chain B: R.23, V.24, V.75, R.80 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.24, B:V.24 Salt bridges: B:R.80 SO4.11: 4 residues within 4Å: Chain B: R.25, L.27, R.39 Ligands: NA.12 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.25, B:R.39 SO4.13: 3 residues within 4Å: Chain B: H.81 Chain C: R.1 Ligands: NA.14 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:R.1, B:H.81

3 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain A: V.97, E.98 Ligands: SO4.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.97 NA.12: 2 residues within 4Å: Chain B: R.39 Ligands: SO4.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.39 NA.14: 2 residues within 4Å: Chain C: F.2 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.2, C:F.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Galperin, M. et al., CD4+T cell-mediated HLA class II cross-restriction in HIV controllers. Sci Immunol (2018)

Release Date

2018-06-06

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
HLA class II histocompatibility antigen, DRB1-11 beta chain: B
Gag polyprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen, DRB1-11 beta chain

Gag polyprotein

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