SMTL ID : 3u4e.2 (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: 24 residues within 4Å: Chain A: T.11, L.12, R.13, S.31, F.32, N.33, K.44, G.118, E.120, 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 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: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 12 residues within 4Å: Chain A: A.17, T.18, I.19, V.27, N.29, Y.46, L.48 Chain B: S.55, F.113, Y.114 Ligands: BMA-MAN.3, BMA-MAN.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.113, B:Y.114 Hydrogen bonds: B:Y.114

1 x BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose(Non-covalent)

BMA-MAN.3: 5 residues within 4Å: Chain B: G.54, S.55, E.56, K.57 Ligands: NAG-NAG.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.54, B:K.57

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

SO4.4: 4 residues within 4Å: Chain C: Q.23, G.70, N.71, T.72 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.23, C:N.71, C:N.71, C:T.72 Water bridges: C:T.72, C:T.72 SO4.5: 2 residues within 4Å: Chain C: S.69, G.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.68, C:G.70 SO4.6: 4 residues within 4Å: Chain C: S.61, R.63, Q.81, E.83 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.61, C:Q.81, C:E.83 Salt bridges: C:R.63 SO4.7: 6 residues within 4Å: Chain B: Q.42, G.43 Chain C: Y.89, T.103, G.104, T.105 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Water bridges: B:G.43 Hydrogen bonds: 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
J

B
A

C
B

V1V2 region of HIV-1 on 1FD6 scaffold

PG9 Heavy Chain

PG9 Light Chain

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