SMTL ID : 4lsp.1

Crystal structure of broadly and potently neutralizing antibody VRC-CH31 in complex with HIV-1 clade A/E gp120 93TH057

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA.1: 4 residues within 4Å: Chain C: T.20, Q.24, N.70, S.72 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.20

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

NAG.2: 2 residues within 4Å: Chain A: E.44, N.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.45 NAG.3: 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, A:T.120, A:T.120, A:H.220 Water bridges: A:N.118 NAG.4: 11 residues within 4Å: Chain A: P.96, K.136, V.138, L.145, N.146, F.243, R.246, C.306, V.307, S.308 Ligands: NAG.13 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 Water bridges: A:D.95, A:D.95, A:R.246 NAG.5: 9 residues within 4Å: Chain A: E.159, N.160, T.162 Chain C: G.28, I.29, G.30, D.32, Q.90, Y.91 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:N.160, A:T.162, C:I.29, C:D.32 Hydrophobic interactions: C:I.29, C:Y.91 Water bridges: C:G.30 NAG.6: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, Q.212, K.216 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.154, A:I.154, A:K.216 Water bridges: A:Q.212, A:Q.212, A:Q.212, A:Q.212 NAG.7: 7 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200, K.303, N.305, V.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.179, A:T.181, A:Y.198, A:K.303 NAG.8: 3 residues within 4Å: Chain A: N.202, T.204, K.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.205 NAG.9: 3 residues within 4Å: Chain A: E.219, N.222, N.223 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.239, A:T.255 NAG.11: 7 residues within 4Å: Chain A: N.259, T.261, C.262, M.268, K.269, G.270, C.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.261, A:T.261, A:K.269 NAG.12: 5 residues within 4Å: Chain A: T.204, T.267, M.268, C.271, N.272 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.267, A:M.268, A:M.268, A:N.272 NAG.13: 5 residues within 4Å: Chain A: K.136, N.146, S.175, N.309 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.136, A:S.175

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

SO4.14: 4 residues within 4Å: Chain A: A.15, K.16, A.17, H.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.17, A:H.18 Salt bridges: A:H.18 SO4.15: 3 residues within 4Å: Chain A: R.195, K.280, K.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.195 Salt bridges: A:K.280 SO4.31: 9 residues within 4Å: Chain B: Q.48, Q.53, L.54 Chain C: T.85, F.87, F.94, G.95, Q.96, G.97 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.48, B:Q.53, B:L.54, C:G.95

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

EDO.16: 12 residues within 4Å: Chain A: N.164, A.165, K.166, T.167, L.315, T.316, G.332, G.333, G.334 Chain B: F.42, W.59 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.316, A:G.334 EDO.17: 11 residues within 4Å: Chain A: I.238, T.316, G.332, G.333, G.334 Chain B: F.42, W.59, N.61, N.64, A.66 Ligands: EDO.16 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.332, A:G.334, B:N.61 Water bridges: A:T.316, B:V.67 EDO.18: 10 residues within 4Å: Chain A: D.235, E.237, I.238, N.286, M.287, W.288 Chain B: N.64, R.81 Ligands: PEG.21, NA.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.235, A:E.237, A:M.287 EDO.19: 7 residues within 4Å: Chain A: A.12, T.34, D.35, P.38, H.100, C.131, T.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.35 EDO.20: 8 residues within 4Å: Chain A: L.9, F.10, C.11, W.26, A.30, Q.60, D.64, Y.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.9 Water bridges: A:D.64, A:D.64 EDO.25: 8 residues within 4Å: Chain B: S.7, G.8, A.10, R.12, V.18, T.19, V.20, T.125 No protein-ligand interaction detected (PLIP) EDO.26: 7 residues within 4Å: Chain A: A.165 Chain B: P.39, E.40, H.41, F.42, H.44, E.115 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.40, B:H.41, B:F.42 Water bridges: B:E.115 EDO.27: 9 residues within 4Å: Chain B: V.2, Q.3, L.4, V.5, K.23, F.24, A.25, E.26 Ligands: EDO.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.26 EDO.28: 7 residues within 4Å: Chain B: V.2, L.4, F.24, R.107, K.110, H.120 Ligands: EDO.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.107 EDO.29: 7 residues within 4Å: Chain B: V.5, Q.6, S.7, S.21, C.22, K.23, T.87 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.6, B:S.21, B:K.23 EDO.32: 3 residues within 4Å: Chain C: K.39, K.42, K.45 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.39, C:K.42, C:K.45

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.21: 14 residues within 4Å: Chain A: S.140, T.141, Q.142, I.238, W.288, L.314, G.333, G.334, N.335, I.336, D.338, N.339 Chain B: N.64 Ligands: EDO.18 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.64, A:N.339, A:N.339 Water bridges: A:Q.142 PEG.22: 9 residues within 4Å: Chain A: D.235, L.236, E.237, Y.251, K.282, I.284, I.285, N.286, Q.293 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.282, A:N.286, A:N.286, A:Q.293

3 x NA: SODIUM ION(Non-functional Binders)

NA.23: 5 residues within 4Å: Chain A: A.5, D.6, N.56, M.57, V.349 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.6, A:M.57 Water bridges: A:N.56, A:V.349 NA.24: 6 residues within 4Å: Chain A: M.287, W.288, G.290 Chain B: T.63, N.64 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.63 NA.30: 6 residues within 4Å: Chain B: S.97, T.100, V.128, V.129, S.130, L.188 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies. Immunity (2013)

Release Date

2013-09-04

Peptides

HIV-1 CLADE A/E STRAIN 93TH057 GP120: A
HEAVY CHAIN OF ANTIBODY VRC-CH31: B
LIGHT CHAIN OF ANTIBODY VRC-CH31: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

HIV-1 CLADE A/E STRAIN 93TH057 GP120

HEAVY CHAIN OF ANTIBODY VRC-CH31

LIGHT CHAIN OF ANTIBODY VRC-CH31

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