SMTL ID : 3ngb.4 (3 other biounits)

Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.1: 3 residues within 4Å: Chain C: I.20, S.63, N.70 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: E.44, N.45 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: N.118, T.120, I.156, H.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.120 NAG.4: 5 residues within 4Å: Chain A: H.42, N.113, D.114, K.115, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.114, A:K.115 NAG.5: 9 residues within 4Å: Chain A: P.96, K.136, V.138, N.146, N.244, R.246, C.306, V.307, S.308 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 NAG.6: 4 residues within 4Å: Chain A: E.159, N.160 Chain C: G.29, S.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.159 NAG.7: 6 residues within 4Å: Chain A: E.153, I.154, N.173, K.174, Q.212, K.216 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.174 Hydrogen bonds: A:I.154, A:Q.212, A:Q.212 Water bridges: A:Q.212 NAG.8: 3 residues within 4Å: Chain A: N.179, E.200, K.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.303 Water bridges: A:N.305, A:N.305 NAG.9: 1 residues within 4Å: Chain A: N.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.202 NAG.10: 3 residues within 4Å: Chain A: T.239, N.253, T.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 NAG.11: 5 residues within 4Å: Chain A: T.255, Q.256, N.259, C.262, G.270 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.256 Water bridges: A:N.260 NAG.12: 2 residues within 4Å: Chain A: S.175, N.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175, A:N.309

3 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.13: 3 residues within 4Å: Chain A: D.193, R.195, K.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.193, A:K.280, A:K.280 BGC.14: 8 residues within 4Å: Chain A: W.53, K.54, E.159, T.167, N.335, K.337, D.338, R.341 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.54, A:K.54, A:T.167, A:N.335, A:D.338, A:D.338 Salt bridges: A:K.337, A:R.341 BGC.17: 3 residues within 4Å: Chain B: K.12, E.16, S.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.12, B:S.17, B:S.17

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.15: 5 residues within 4Å: Chain A: L.9, F.10, C.11, D.64, Y.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.9, A:C.11 TRS.16: 8 residues within 4Å: Chain A: L.79, T.80, G.81, T.291, G.292, Q.293 Chain B: D.73, Y.75 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:L.79, A:G.81, A:N.286, A:G.292, A:Q.293, B:D.73, B:Y.75 Water bridges: B:V.74 TRS.18: 4 residues within 4Å: Chain B: G.170, T.191 Chain C: N.134, D.166 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Water bridges: B:H.172, C:N.134 Hydrogen bonds: C:N.134, C:D.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Science (2010)

Release Date

2010-07-07

Peptides

Envelope glycoprotein gp160: A
Antigen binding fragment of heavy chain: Antibody VRC01: B
Antigen binding fragment of light chain: Antibody VRC01: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

Envelope glycoprotein gp160

Antigen binding fragment of heavy chain: Antibody VRC01

Antigen binding fragment of light chain: Antibody VRC01

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