SMTL ID : 3se8.1

Crystal structure of broadly and potently neutralizing antibody VRC03 in complex with HIV-1 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: E.44, N.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.44 NAG.2: 9 residues within 4Å: Chain A: N.118, T.120, G.121, P.122, I.156, R.157, S.158, L.161, H.220 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118 Water bridges: A:N.118, A:T.120, A:S.158, A:S.158 NAG.3: 4 residues within 4Å: Chain A: N.113, D.114, K.124, N.125 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.125 Hydrogen bonds: A:N.125 Water bridges: A:E.40, A:K.115 NAG.4: 14 residues within 4Å: Chain A: D.95, P.96, K.136, V.138, L.145, N.146, F.243, N.244, C.245, R.246, C.306, V.307, S.308 Ligands: NAG.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.146, A:R.246, A:S.308 Water bridges: A:D.95, A:R.246, A:N.305, A:V.307 NAG.5: 7 residues within 4Å: Chain A: E.159, N.160 Chain C: N.30, A.31, D.49, F.90 Ligands: SO4.14 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:A.31, A:N.160, A:N.160 Water bridges: C:D.49, A:E.159 NAG.6: 8 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, Q.212, K.216 Ligands: SO4.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.154, A:N.173 Water bridges: A:E.152 NAG.7: 8 residues within 4Å: Chain A: E.177, N.179, T.181, Y.198, E.200, K.303, N.305, V.307 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.181, A:K.303 Water bridges: A:T.181, A:T.181, A:N.305 NAG.8: 5 residues within 4Å: Chain A: N.202, T.204, K.205, G.273, T.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.205 Water bridges: A:N.202, A:N.202 NAG.9: 5 residues within 4Å: Chain A: L.236, T.239, M.240, N.253, T.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.253 Water bridges: A:T.255, A:T.255 NAG.10: 9 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261, C.262, M.268, K.269, G.270, C.271 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.256 Water bridges: A:N.259, A:N.259 NAG.11: 6 residues within 4Å: Chain A: K.136, N.146, L.149, S.175, N.309 Ligands: NAG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.175 Water bridges: A:S.175, A:N.309, A:N.309, A:N.309

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

SO4.12: 3 residues within 4Å: Chain A: N.335, K.337, R.341 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.335 Water bridges: A:R.341 Salt bridges: A:K.337, A:R.341 SO4.13: 4 residues within 4Å: Chain A: K.174, K.208, Q.212 Ligands: NAG.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.212 Salt bridges: A:K.174, A:K.208 SO4.14: 7 residues within 4Å: Chain A: N.163 Chain B: G.113, D.114, F.115, P.116 Chain C: F.90 Ligands: NAG.5 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Water bridges: C:T.33, C:F.90 Hydrogen bonds: B:D.114, B:F.115, A:N.163 SO4.15: 7 residues within 4Å: Chain B: G.66, R.67, V.68, S.69, E.89, F.90, S.91 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.91, B:S.91 SO4.16: 4 residues within 4Å: Chain A: A.165, T.167, N.335 Chain B: K.52 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.167, A:N.335 Water bridges: B:S.33, B:S.33, B:K.52 Salt bridges: B:K.52 SO4.20: 6 residues within 4Å: Chain C: R.38, R.44, G.56, P.58, R.60, F.61 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.38 Water bridges: C:G.56, C:R.60, C:R.60, C:D.81 Salt bridges: C:R.44, C:R.60 SO4.21: 6 residues within 4Å: Chain B: P.140, K.226, K.231 Chain C: S.116, D.117, E.118 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.117, C:E.118 Salt bridges: B:K.231 SO4.22: 3 residues within 4Å: Chain C: G.29, S.66, G.67 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.29, C:S.66, C:G.67

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

EDO.17: 8 residues within 4Å: Chain B: A.142, P.143, S.144, A.153, A.154 Chain C: F.111, I.112, F.113 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.144, B:A.154, B:A.154, C:I.112, C:I.112 EDO.19: 7 residues within 4Å: Chain B: L.39, P.41, T.98, A.99, E.100, V.125, V.127 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.39 Water bridges: B:E.100

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

TRS.18: 5 residues within 4Å: Chain B: V.167, T.168, V.169, T.182, L.195 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.167, B:V.169, B:V.169 Water bridges: B:T.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, X. et al., Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Science (2011)

Release Date

2011-08-10

Peptides

HIV-1 Clade AE strain 93TH057 gp120: A
Heavy chain of antibody VRC03: B
Light chain of antibody VRC03: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

HIV-1 Clade AE strain 93TH057 gp120

Heavy chain of antibody VRC03

Light chain of antibody VRC03

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