SMTL ID : 3u2s.2 (1 other biounit)

Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain ZM109

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: 21 residues within 4Å: Chain A: D.103, R.105, Y.110, Y.118, N.119, Y.120, H.121 Chain B: Y.32, E.33, S.34, D.52, L.93, R.97, R.99 Chain C: T.11, L.12, A.13, S.31, F.32, N.33, K.44 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.103, A:Y.118 Hydrogen bonds: A:D.103 Water bridges: A:R.105

1 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.2: 9 residues within 4Å: Chain A: G.41, Q.42, G.43 Chain B: D.87, Y.89, T.103, G.104, T.105, K.106 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.87 Hydrogen bonds: B:T.103, A:G.41

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

SO4.3: 2 residues within 4Å: Chain B: R.56, N.62 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.62 Water bridges: B:V.60 Salt bridges: B:R.56 SO4.4: 1 residues within 4Å: Chain B: S.204 No protein-ligand interaction detected (PLIP) SO4.5: 4 residues within 4Å: Chain B: Q.23, G.70, N.71, T.72 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.71, B:T.72

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 7 residues within 4Å: Chain A: D.53, S.55, F.113, Y.114 Chain C: N.46, T.48, Y.50 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.113 Hydrogen bonds: A:Y.114, C:N.46

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

PG9 heavy chain: A
PG9 light chain: B
Envelope glycoprotein gp120: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

PG9 heavy chain

PG9 light chain

Envelope glycoprotein gp120

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