SMTL ID : 3ecb.1

Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human immunodeficiency virus envelope glycoprotein 120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 2 residues within 4Å: Chain A: S.38, D.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.39 EDO.2: 9 residues within 4Å: Chain A: W.204, R.234, W.244 Chain B: V.10, Y.11, D.97, M.100 Ligands: EDO.6, EDO.7 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.234, A:R.234, A:W.244 Water bridges: B:S.12 EDO.3: 6 residues within 4Å: Chain A: W.114, W.147, A.152, D.156 Chain C: R.5, V.8 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.156, C:R.5, C:R.5 EDO.4: 3 residues within 4Å: Chain A: V.12, R.21 Chain B: H.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.14, A:R.21 EDO.6: 6 residues within 4Å: Chain B: Q.9, V.10, Y.95, W.96, D.97 Ligands: EDO.2 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.10, B:D.97, B:D.97 Water bridges: B:I.8, A:R.234 EDO.7: 8 residues within 4Å: Chain A: L.206, R.234, Q.242 Chain B: Y.11, S.12, H.14, P.15 Ligands: EDO.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.234, A:Q.242, B:S.12 Water bridges: A:Q.242

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain A: C.121 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, R. et al., Structural basis of the CD8alphabeta/MHC class i interaction: focused recognition orients CD8beta to a T cell proximal position. J.Immunol. (2009)

Release Date

2009-07-14

Peptides

H-2 class I histocompatibility antigen, D-D alpha chain: A
Beta-2 microglobulin: B
Peptide P18-I10 from HIV gp160: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
P

H-2 class I histocompatibility antigen, D-D alpha chain

Beta-2 microglobulin

Peptide P18-I10 from HIV gp160

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