SMTL ID : 3u4e.1 (1 other biounit)

Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain CAP45

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 23 residues within 4Å: Chain A: T.11, L.12, R.13, S.31, F.32, N.33, K.44, V.121 Chain B: D.103, R.105, Y.110, Y.118, N.119, Y.120, H.121 Chain C: Y.32, E.33, S.34, D.52, K.55, L.93, R.97, R.99 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.103, B:Y.118 Hydrogen bonds: B:D.103

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.2: 15 residues within 4Å: Chain A: A.17, T.18, I.19, V.27, N.29, Y.46, L.48 Chain B: D.53, G.54, S.55, E.56, K.57, N.73, F.113, Y.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.54, B:K.57 Water bridges: B:K.57 Hydrophobic interactions: B:F.113, B:Y.114

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

SO4.3: 6 residues within 4Å: Chain A: T.3, F.4, K.5, T.110, K.111, T.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.3, A:T.112 SO4.4: 3 residues within 4Å: Chain C: S.61, R.63, Q.81 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.61, C:S.61, C:Q.81 Salt bridges: C:R.63 SO4.5: 1 residues within 4Å: Chain C: K.190 2 PLIP interactions: 2 interactions with chain C Water bridges: C:K.190 Salt bridges: C:K.190 SO4.6: 4 residues within 4Å: Chain C: Q.23, G.70, N.71, T.72 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.23, C:N.71, C:N.71, C:N.71, C:T.72 SO4.7: 8 residues within 4Å: Chain C: E.85, T.108, V.109, G.111, Q.112, Y.144, K.170, Y.176 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.111, C:G.111, C:Q.112, C:Y.144 Water bridges: C:E.85, C:K.170, C:K.170, C:N.174, C:N.174, C:Y.176 Salt bridges: C:K.170 SO4.8: 4 residues within 4Å: Chain C: G.12, S.13, Q.16, L.110 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.13, C:S.13, C:Q.16 SO4.9: 5 residues within 4Å: Chain B: S.195 Chain C: A.161, G.162, V.163, E.164 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.195, C:G.162 SO4.10: 6 residues within 4Å: Chain B: G.41, G.43 Chain C: D.87, Y.89, T.103, G.104 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.41, C:Y.89, C:G.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McLellan, J.S. et al., Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. Nature (2011)

Release Date

2011-11-30

Peptides

V1V2 region of HIV-1 on 1FD6 scaffold: A
PG9 Heavy Chain: B
PG9 Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

V1V2 region of HIV-1 on 1FD6 scaffold

PG9 Heavy Chain

PG9 Light Chain

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