SMTL ID : 4jam.1 (1 other biounit)

Crystal structure of broadly neutralizing anti-hiv-1 antibody ch103

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.151, D.152, Q.179 Chain B: K.126, S.176 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.176, A:Q.179 Water bridges: B:A.127, B:T.128, A:K.151, A:K.151, A:K.151 Salt bridges: B:K.126, A:K.151 SO4.2: 5 residues within 4Å: Chain A: P.131, K.217 Chain B: S.119, E.120 Ligands: EDO.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.220 Salt bridges: A:K.217 Water bridges: B:E.120 SO4.3: 5 residues within 4Å: Chain A: G.30, G.31, F.52, H.53, R.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.31 Water bridges: A:H.53 Salt bridges: A:H.53, A:R.100 SO4.4: 8 residues within 4Å: Chain A: Q.179, S.180 Chain B: G.155, V.156, E.157, S.176 Ligands: EDO.7, EDO.8 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.155, B:S.176, A:Q.179, A:S.180 Water bridges: B:V.156, B:V.156, B:S.176, A:S.181 SO4.5: 4 residues within 4Å: Chain A: H.172, T.173 Chain B: Q.164, S.165 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.165 Water bridges: A:T.173 Salt bridges: A:H.172 SO4.6: 3 residues within 4Å: Chain A: H.53, T.54, T.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.53, A:T.73 Salt bridges: A:H.53 SO4.13: 2 residues within 4Å: Chain A: K.137 Chain B: K.201 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Salt bridges: A:K.137, B:K.201 Water bridges: B:K.201, B:K.201, B:K.201, B:K.201

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

EDO.7: 10 residues within 4Å: Chain A: L.149, K.151, V.177, Q.179, S.185 Chain B: T.128, E.157, Y.174, S.176 Ligands: SO4.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.151, A:S.185, B:S.176 Water bridges: A:D.152, B:S.176 EDO.8: 8 residues within 4Å: Chain A: A.87, A.88, T.90, L.178, Q.179, S.180 Chain B: E.157 Ligands: SO4.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:E.157, A:L.178 EDO.9: 8 residues within 4Å: Chain A: P.131, A.133, K.217, K.218, V.219, E.220, K.222 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.218, A:E.220 EDO.10: 5 residues within 4Å: Chain A: P.127, S.128, V.129, V.215 Ligands: GOL.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.129, A:V.129 EDO.11: 4 residues within 4Å: Chain A: Q.102, L.103, V.104 Chain B: W.86 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.102, A:L.103, A:V.104 Water bridges: A:G.101, B:W.86 EDO.14: 10 residues within 4Å: Chain B: Y.1, L.3, G.23, A.24, S.25, T.26, V.85, W.86, D.87, S.88 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.23, B:S.25, B:D.87, B:D.87 Water bridges: B:T.26

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 6 residues within 4Å: Chain A: V.129, F.130, P.131, K.217 Chain B: E.120 Ligands: EDO.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.120, A:K.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liao, H.X. et al., Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature (2013)

Release Date

2013-04-03

Peptides

ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103: A
ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103

ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103

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