SMTL ID : 2b4c.1 (1 other biounit)

Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 3 residues within 4Å: Chain A: N.134 Chain B: Q.33, K.90 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.90 Hydrogen bonds: B:Q.33, B:Q.33, B:K.90, A:N.134

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

NAG.2: 6 residues within 4Å: Chain A: R.110, V.112, N.120, C.234, S.298, S.299 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.112 NAG.3: 5 residues within 4Å: Chain A: T.155, H.187, N.189, T.265, T.267 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.187, A:T.265 NAG.4: 4 residues within 4Å: Chain A: N.218, H.219, N.248, R.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.219, A:R.321

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

SO4.5: 4 residues within 4Å: Chain A: A.62, C.63, P.64 Chain D: I.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.63 SO4.6: 3 residues within 4Å: Chain C: P.8, G.9, T.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.9, C:T.10 SO4.10: 4 residues within 4Å: Chain D: G.28, T.29, Y.33, R.99 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.29, D:T.29, D:Y.33 Salt bridges: D:R.99 SO4.11: 5 residues within 4Å: Chain D: E.11, K.13, S.18, V.19, Q.20 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.20, D:Q.20 Salt bridges: D:K.13 SO4.12: 2 residues within 4Å: Chain D: K.225, D.227 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.225

3 x XYL: Xylitol(Non-covalent)

XYL.7: 3 residues within 4Å: Chain D: S.8, G.9, K.220 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.9, D:K.220 XYL.8: 5 residues within 4Å: Chain D: K.24, A.25, G.27, G.28, S.78 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.24, D:K.24, D:G.27, D:G.28 XYL.9: 3 residues within 4Å: Chain D: Q.124, N.218, K.225 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.124, D:K.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, C.C. et al., Structure of a V3-containing HIV-1 gp120 core. Science (2005)

Release Date

2005-11-15

Peptides

envelope glycoprotein: A
T-cell surface glycoprotein CD4: B
anti-HIV-1 gp120 immunoglobulin X5 light chain: C
anti-HIV-1 gp120 immunoglobulin X5 heavy chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
C

C
L

D
H

envelope glycoprotein

T-cell surface glycoprotein CD4

anti-HIV-1 gp120 immunoglobulin X5 light chain

anti-HIV-1 gp120 immunoglobulin X5 heavy chain

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