SMTL ID : 1tjg.1

Crystal Structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a gp41 7mer epitope

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLU- LEU- ASP- LYS- TRP- ALA- SER: Envelope glycoprotein GP41(Non-covalent)

GLU-LEU-ASP-LYS-TRP-ALA-SER.1: 14 residues within 4Å: Chain A: L.91, H.92, F.93, Y.94, H.96 Chain B: G.33, Y.54, D.56, D.58, R.60, R.100, P.103, R.113, V.116 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:Y.54, B:V.116, A:F.93 Hydrogen bonds: B:D.56, B:D.58, B:R.113, A:H.92, A:Y.94, A:Y.94, A:Y.94 Water bridges: B:R.100, A:L.91, A:H.92 Salt bridges: B:R.60, B:R.100, B:R.113, A:H.96

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

EDO.2: 5 residues within 4Å: Chain A: S.10, L.11, S.12, P.141, E.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.10 Water bridges: A:R.142 EDO.3: 4 residues within 4Å: Chain A: E.187, K.188, K.190, R.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.187, A:R.211 EDO.7: 5 residues within 4Å: Chain A: T.178 Chain B: L.160, V.188, S.196, S.198 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.198, A:T.178 Water bridges: B:S.198, B:S.198, A:S.176

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

IPA.4: 1 residues within 4Å: Chain A: L.54 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.55 IPA.5: 4 residues within 4Å: Chain A: S.65, G.66, E.70, T.72 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.72 Hydrogen bonds: A:E.70 IPA.6: 5 residues within 4Å: Chain A: V.150, Q.155, L.181, D.185, H.189 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.150, A:L.181, A:L.181 Water bridges: A:D.185, A:D.185 IPA.8: 3 residues within 4Å: Chain B: S.139, V.140, V.226 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.226 Hydrogen bonds: B:V.140 Water bridges: B:P.138 IPA.9: 5 residues within 4Å: Chain A: D.167, K.169 Chain B: G.181, V.182, H.183 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.182 IPA.10: 1 residues within 4Å: Chain B: G.108 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.108 IPA.11: 4 residues within 4Å: Chain B: K.136, G.137, P.138, S.139 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.136 Hydrogen bonds: B:P.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ofek, G. et al., Structure and mechanistic analysis of the Anti-Human Immunodeficiency Virus Type 1 antibody 2F5 in complex with its gp41 epitope. J.Virol. (2004)

Release Date

2004-10-05

Peptides

FAB 2F5 Light Chain: A
FAB 2F5 Heavy Chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

FAB 2F5 Light Chain

FAB 2F5 Heavy Chain

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