SMTL ID : 6cpl.1

Crystal structure of DR11 presenting the gag293 epitope

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.2

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

NAG.2: 3 residues within 4Å: Chain A: S.77, N.78 Chain B: L.53 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.53 Hydrogen bonds: A:N.78 NAG.6: 2 residues within 4Å: Chain B: N.19, E.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.22

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

SO4.3: 5 residues within 4Å: Chain A: T.41, W.43, A.52, S.53, F.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.54 Water bridges: A:T.41, A:T.41, A:F.54 SO4.4: 2 residues within 4Å: Chain A: K.111, R.140 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.111, A:R.140 SO4.9: 5 residues within 4Å: Chain B: E.22, R.23, V.24, V.75, R.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.24 Salt bridges: B:R.80 SO4.10: 3 residues within 4Å: Chain B: R.25, L.27, R.39 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.41 Salt bridges: B:R.25, B:R.39 SO4.11: 3 residues within 4Å: Chain B: K.65, L.68, R.72 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.65, B:R.72

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

NA.5: 3 residues within 4Å: Chain A: R.50, F.51, A.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.51 NA.12: 2 residues within 4Å: Chain B: E.176, P.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.176 NA.13: 4 residues within 4Å: Chain A: S.53, F.54, E.55 Chain C: Y.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.53, A:E.55, C:Y.9

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 5 residues within 4Å: Chain A: F.108, F.148 Chain B: L.147, I.148, H.149 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:H.149, A:F.108, A:F.148 Hydrogen bonds: B:H.149 ACT.8: 3 residues within 4Å: Chain B: V.91, Q.92, R.94 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.92 Salt bridges: B:R.94

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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