SMTL ID : 1g9m.1

HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG-FUC.1: 7 residues within 4Å: Chain A: E.151, N.153, N.161, S.163, T.242, R.273, S.275 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.161, A:T.242 Hydrogen bonds: A:S.163 Water bridges: A:E.151, A:E.151, A:S.163 NAG-FUC.2: 1 residues within 4Å: Chain A: N.292 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.292

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

NAG.3: 1 residues within 4Å: Chain A: N.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.10 NAG.4: 2 residues within 4Å: Chain A: V.49, N.55 No protein-ligand interaction detected (PLIP) NAG.5: 8 residues within 4Å: Chain A: C.86, N.88, K.89, T.90, P.96, C.97, T.98, N.99 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.88 Hydrogen bonds: A:P.96, A:T.98 NAG.6: 6 residues within 4Å: Chain A: T.90, F.91, N.92, T.94, G.95, P.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.92 Water bridges: A:P.96 NAG.7: 3 residues within 4Å: Chain A: L.8, N.87, N.99 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.87 NAG.8: 4 residues within 4Å: Chain A: R.110, N.120, S.275, S.276 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.110, A:R.110 Water bridges: A:R.273, A:S.275 NAG.9: 4 residues within 4Å: Chain A: N.134, T.136, D.137 Chain B: Q.33 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.134, A:T.136, A:D.137, B:Q.33 NAG.10: 6 residues within 4Å: Chain A: E.126, E.127, V.128, N.147, Q.173, K.177 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.127 Hydrogen bonds: A:V.128, A:Q.173 Water bridges: A:E.127 NAG.11: 3 residues within 4Å: Chain A: N.168, K.172, W.224 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.224 NAG.12: 4 residues within 4Å: Chain A: N.215, T.217, Q.218, P.246 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.246 Hydrogen bonds: A:N.215, A:T.217, A:Q.218 Water bridges: A:Q.218 NAG.13: 1 residues within 4Å: Chain A: N.221 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.221, A:N.221 NAG.14: 3 residues within 4Å: Chain A: S.149, S.275, N.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.275

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.15: 5 residues within 4Å: Chain A: V.113, S.204, F.205, F.211, W.256 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.254, A:W.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwong, P.D. et al., Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure Fold.Des. (2000)

Release Date

2000-12-27

Peptides

ENVELOPE GLYCOPROTEIN GP120: A
T-CELL SURFACE GLYCOPROTEIN CD4: B
ANTIBODY 17B, LIGHT CHAIN: C
ANTIBODY 17B, HEAVY CHAIN: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
C

C
L

D
H

ENVELOPE GLYCOPROTEIN GP120

T-CELL SURFACE GLYCOPROTEIN CD4

ANTIBODY 17B, LIGHT CHAIN

ANTIBODY 17B, HEAVY CHAIN

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