SMTL ID : 1rzf.1

Crystal structure of Human anti-HIV-1 GP120-reactive antibody E51

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: K.114, A.116, H.201, E.202, S.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.201, A:S.204, A:S.204 GOL.2: 7 residues within 4Å: Chain A: Q.38, K.46, P.60, R.62, F.63, G.82, D.83 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.38, A:Q.38, A:K.46, A:R.62, A:D.83 Water bridges: A:R.62 GOL.3: 8 residues within 4Å: Chain A: S.118, V.119, T.120, L.139, I.140, S.141 Chain B: F.187, T.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.118, A:T.120 GOL.4: 8 residues within 4Å: Chain A: T.108, V.109, L.110, G.111, Q.112, K.114, Y.144, P.145 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.112, A:Q.112 Water bridges: A:E.84, A:Q.112, A:Y.144 GOL.5: 6 residues within 4Å: Chain A: A.147, V.148, T.149, T.200, E.202, G.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.148, A:G.203 Water bridges: A:E.202, A:E.202 GOL.6: 5 residues within 4Å: Chain A: R.55, P.56, S.57, G.58, I.59 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.55, A:R.55, A:G.58, A:I.59, A:I.59 GOL.7: 3 residues within 4Å: Chain A: P.113, Y.144, N.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.113, A:N.174 GOL.8: 6 residues within 4Å: Chain A: S.66, K.67, S.68, S.71, A.72, T.73 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.66, A:S.68, A:S.71, A:S.71, A:T.73 Water bridges: A:S.71 GOL.9: 7 residues within 4Å: Chain A: K.17, T.19, S.64, G.65, S.66, T.73, G.75 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.17, A:S.64, A:S.64, A:G.65, A:G.75 GOL.12: 11 residues within 4Å: Chain A: D.33, S.35, Y.37, G.90, T.91, W.92, V.99 Chain B: G.116, Y.119, D.120, M.121 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.33, A:S.35, A:Y.37 Water bridges: A:W.92, A:W.92 GOL.13: 4 residues within 4Å: Chain B: S.141, V.142, V.228, K.230 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.140, B:V.142, B:K.230, B:K.230 GOL.14: 6 residues within 4Å: Chain B: R.38, Q.39, A.40, Q.43, G.44, E.46 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.38, B:A.40, B:Q.43, B:G.44 Water bridges: B:K.63, B:K.63 GOL.15: 3 residues within 4Å: Chain B: G.44, L.45, E.46 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.44, B:E.46 Water bridges: B:L.45, A:F.101, A:F.101

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

IPA.10: 4 residues within 4Å: Chain A: Q.39, P.41, G.42 Chain B: G.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.42 IPA.11: 7 residues within 4Å: Chain A: D.86, Y.88, G.103, G.104 Chain B: G.42, Q.43, G.44 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, C.C. et al., Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120. Proc.Natl.Acad.Sci.USA (2004)

Release Date

2004-02-03

Peptides

Fab E51 light chain: A
Fab E51 heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Fab E51 light chain

Fab E51 heavy chain

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