SMTL ID : 2b4c.2 (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-4-4-4-4-mer

Ligands

4 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 NAG-FUC.13: 3 residues within 4Å: Chain E: N.134 Chain F: Q.33, K.90 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:K.90 Hydrogen bonds: F:Q.33, F:Q.33, F:K.90, E:N.134 NAG-FUC.25: 3 residues within 4Å: Chain I: N.134 Chain J: Q.33, K.90 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:K.90 Hydrogen bonds: J:Q.33, J:Q.33, J:K.90, I:N.134 NAG-FUC.37: 3 residues within 4Å: Chain M: N.134 Chain N: Q.33, K.90 5 PLIP interactions: 4 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: N:K.90 Hydrogen bonds: N:Q.33, N:Q.33, N:K.90, M:N.134

12 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 NAG.14: 6 residues within 4Å: Chain E: R.110, V.112, N.120, C.234, S.298, S.299 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.112 NAG.15: 5 residues within 4Å: Chain E: T.155, H.187, N.189, T.265, T.267 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.187, E:T.265 NAG.16: 4 residues within 4Å: Chain E: N.218, H.219, N.248, R.321 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.219, E:R.321 NAG.26: 6 residues within 4Å: Chain I: R.110, V.112, N.120, C.234, S.298, S.299 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:V.112 NAG.27: 5 residues within 4Å: Chain I: T.155, H.187, N.189, T.265, T.267 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:H.187, I:T.265 NAG.28: 4 residues within 4Å: Chain I: N.218, H.219, N.248, R.321 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:H.219, I:R.321 NAG.38: 6 residues within 4Å: Chain M: R.110, V.112, N.120, C.234, S.298, S.299 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:V.112 NAG.39: 5 residues within 4Å: Chain M: T.155, H.187, N.189, T.265, T.267 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:H.187, M:T.265 NAG.40: 4 residues within 4Å: Chain M: N.218, H.219, N.248, R.321 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:H.219, M:R.321

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

SO4.5: 9 residues within 4Å: Chain A: A.62, C.63, P.64 Chain D: I.55 Chain I: A.62, C.63, P.64 Chain L: I.55 Ligands: SO4.29 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain C: P.8, G.9, T.10 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain D: G.28, T.29, Y.33, R.99 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain D: E.11, K.13, S.18, V.19, Q.20 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain D: K.225, D.227 Chain H: K.225, D.227 Ligands: SO4.24 Ligand excluded by PLIP SO4.17: 9 residues within 4Å: Chain E: A.62, C.63, P.64 Chain H: I.55 Chain M: A.62, C.63, P.64 Chain P: I.55 Ligands: SO4.41 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain G: P.8, G.9, T.10 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain H: G.28, T.29, Y.33, R.99 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain H: E.11, K.13, S.18, V.19, Q.20 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain D: K.225, D.227 Chain H: K.225, D.227 Ligands: SO4.12 Ligand excluded by PLIP SO4.29: 9 residues within 4Å: Chain A: A.62, C.63, P.64 Chain D: I.55 Chain I: A.62, C.63, P.64 Chain L: I.55 Ligands: SO4.5 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain K: P.8, G.9, T.10 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain L: G.28, T.29, Y.33, R.99 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain L: E.11, K.13, S.18, V.19, Q.20 Ligand excluded by PLIP SO4.36: 5 residues within 4Å: Chain L: K.225, D.227 Chain P: K.225, D.227 Ligands: SO4.48 Ligand excluded by PLIP SO4.41: 9 residues within 4Å: Chain E: A.62, C.63, P.64 Chain H: I.55 Chain M: A.62, C.63, P.64 Chain P: I.55 Ligands: SO4.17 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain O: P.8, G.9, T.10 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain P: G.28, T.29, Y.33, R.99 Ligand excluded by PLIP SO4.47: 5 residues within 4Å: Chain P: E.11, K.13, S.18, V.19, Q.20 Ligand excluded by PLIP SO4.48: 5 residues within 4Å: Chain L: K.225, D.227 Chain P: K.225, D.227 Ligands: SO4.36 Ligand excluded by PLIP

12 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: 8 residues within 4Å: Chain D: K.24, A.25, G.27, G.28, S.78 Chain L: K.24, A.76 Ligands: XYL.32 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain L Hydrogen bonds: D:K.24, D:K.24, D:G.27, D:G.28, L:K.24, L:K.24 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 XYL.19: 3 residues within 4Å: Chain H: S.8, G.9, K.220 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:G.9, H:K.220 XYL.20: 8 residues within 4Å: Chain H: K.24, A.25, G.27, G.28, S.78 Chain P: K.24, A.76 Ligands: XYL.44 6 PLIP interactions: 4 interactions with chain H, 2 interactions with chain P Hydrogen bonds: H:K.24, H:K.24, H:G.27, H:G.28, P:K.24, P:K.24 XYL.21: 3 residues within 4Å: Chain H: Q.124, N.218, K.225 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Q.124, H:K.225 XYL.31: 3 residues within 4Å: Chain L: S.8, G.9, K.220 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:G.9, L:K.220 XYL.32: 8 residues within 4Å: Chain D: K.24, A.76 Chain L: K.24, A.25, G.27, G.28, S.78 Ligands: XYL.8 6 PLIP interactions: 4 interactions with chain L, 2 interactions with chain D Hydrogen bonds: L:K.24, L:K.24, L:G.27, L:G.28, D:K.24, D:K.24 XYL.33: 3 residues within 4Å: Chain L: Q.124, N.218, K.225 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:Q.124, L:K.225 XYL.43: 3 residues within 4Å: Chain P: S.8, G.9, K.220 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:G.9, P:K.220 XYL.44: 8 residues within 4Å: Chain H: K.24, A.76 Chain P: K.24, A.25, G.27, G.28, S.78 Ligands: XYL.20 6 PLIP interactions: 2 interactions with chain H, 4 interactions with chain P Hydrogen bonds: H:K.24, H:K.24, P:K.24, P:K.24, P:G.27, P:G.28 XYL.45: 3 residues within 4Å: Chain P: Q.124, N.218, K.225 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:Q.124, P: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: AEIM
T-cell surface glycoprotein CD4: BFJN
anti-HIV-1 gp120 immunoglobulin X5 light chain: CGKO
anti-HIV-1 gp120 immunoglobulin X5 heavy chain: DHLP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

E
G

I
G

M
G

B
C

F
C

J
C

N
C

C
L

G
L

K
L

O
L

D
H

H
H

L
H

P
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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