SMTL ID : 6cqn.1

Crystal structure of F5 TCR -DR11-RQ13 peptide complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.78 No protein-ligand interaction detected (PLIP) NAG.2: 4 residues within 4Å: Chain A: N.118, E.166, W.168 Chain B: D.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.166 Hydrogen bonds: A:W.168 Water bridges: A:W.168

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

SO4.3: 1 residues within 4Å: Chain A: E.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.101 SO4.5: 2 residues within 4Å: Chain B: E.46, R.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.46, B:E.46, B:R.72 SO4.6: 2 residues within 4Å: Chain A: P.16 Chain B: R.4 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.4 SO4.9: 1 residues within 4Å: Chain E: E.3 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.3

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: S.53, F.54 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain D: V.49, K.57 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 5 residues within 4Å: Chain B: H.81 Chain C: R.1, F.2 Chain D: S.28, N.29 No protein-ligand interaction detected (PLIP)

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
Peptide from Capsid protein p24: C
F5 alpha chain: D
F5 beta chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen, DRB1-11 beta chain

Peptide from Capsid protein p24

F5 alpha chain

F5 beta chain

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