SMTL ID : 3se9.1

Crystal structure of broadly and potently neutralizing antibody VRC-PG04 in complex with HIV-1 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 9 residues within 4Å: Chain A: N.118, T.120, G.121, P.122, I.156, S.158, L.161, H.220 Ligands: CL.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118 Water bridges: A:N.118, A:N.118, A:T.120, A:H.220 NAG.2: 6 residues within 4Å: Chain A: E.40, H.42, N.113, K.115, N.125, S.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.40, A:N.113, A:K.115, A:N.125, A:S.127 NAG.3: 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.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 Water bridges: A:D.95, A:V.307 NAG.4: 9 residues within 4Å: Chain A: E.159, N.160, T.162 Chain B: G.107, G.109 Chain C: G.29, H.30, L.89 Ligands: GOL.16 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:G.107, C:H.30, A:N.160, A:T.162 Water bridges: B:G.109 Hydrophobic interactions: C:L.89 NAG.5: 8 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, Q.212, K.216 Ligands: SO4.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.153, A:E.153, A:I.154, A:N.173 NAG.6: 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:K.303 Water bridges: A:N.305 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.202, A:K.205 Water bridges: A:T.274 NAG.8: 5 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 Ligands: CL.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 NAG.9: 8 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261, C.262, M.268, G.270, C.271 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.256 Hydrogen bonds: A:G.270 NAG.10: 6 residues within 4Å: Chain A: N.146, L.149, S.175, V.307, N.309 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.146

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

SO4.11: 4 residues within 4Å: Chain A: N.335, K.337, R.341 Chain B: Y.104 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.335 Water bridges: A:N.335, A:K.337, A:K.337, A:R.341, A:R.341 Salt bridges: A:K.337, A:R.341 SO4.12: 5 residues within 4Å: Chain A: R.195, I.281, K.282, Q.283, I.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.283, A:Q.283, A:I.284 Salt bridges: A:R.195, A:K.282 SO4.13: 4 residues within 4Å: Chain A: K.174, K.208, Q.212 Ligands: NAG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.212 Salt bridges: A:K.174, A:K.208 SO4.33: 7 residues within 4Å: Chain B: P.135, K.221, K.226 Chain C: S.115, D.116, E.117, Q.118 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.116, C:E.117 Salt bridges: B:K.221 SO4.34: 3 residues within 4Å: Chain C: R.83, R.97, R.136 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.97 Salt bridges: C:R.83, C:R.136

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 8 residues within 4Å: Chain A: L.9, F.10, C.11, W.26, A.30, D.64, Y.101 Ligands: CL.26 2 PLIP interactions: 2 interactions with chain A Water bridges: A:C.11, A:D.64 GOL.15: 12 residues within 4Å: Chain A: D.114, K.115, N.116, F.117, A.150, E.151, E.152, I.155, R.157, H.171, Y.345, K.346 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.117, A:E.151, A:R.157, A:Y.345, A:K.346 GOL.16: 5 residues within 4Å: Chain A: N.160, L.161, T.162 Ligands: NAG.4, CL.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.160, A:T.162, A:T.162 GOL.17: 7 residues within 4Å: Chain A: G.81, G.290, T.291, G.292 Chain B: R.76, D.77, F.79 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.76, B:D.77, A:G.81, A:G.290 Water bridges: A:L.79

18 x CL: CHLORIDE ION(Non-functional Binders)

CL.18: 6 residues within 4Å: Chain A: P.230, P.231, N.253, T.254, T.255 Ligands: NAG.8 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: A.15, T.28, P.33 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: S.158, N.160, L.161 Ligands: NAG.1, GOL.16 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain A: I.66, W.69, D.70, Q.289 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain A: H.100, H.133, G.134 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: W.26, H.29, A.30, Q.71 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain A: P.183, S.184, K.303 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain A: I.155, I.156, K.216, H.220 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain A: T.8, L.9, F.10 Ligands: GOL.14 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: S.63, P.64, D.65 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain B: A.41, P.42, Q.44, G.91 Ligand excluded by PLIP CL.30: 6 residues within 4Å: Chain B: P.138, S.139, K.141, A.148, A.149 Chain C: F.110 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: T.163, V.164, T.177 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain C: S.27, Y.28, K.67 Ligand excluded by PLIP CL.36: 6 residues within 4Å: Chain C: K.139, Q.141, E.189, V.190, T.191, P.198 Ligand excluded by PLIP CL.37: 6 residues within 4Å: Chain B: F.134, K.155, D.156 Chain C: Q.118, S.121, T.123 Ligand excluded by PLIP CL.38: 6 residues within 4Å: Chain C: S.61, G.62, S.63, T.70, L.71, T.72 Ligand excluded by PLIP CL.39: 4 residues within 4Å: Chain C: T.5, S.7, S.22, T.24 Ligand excluded by PLIP

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

BU3.27: 10 residues within 4Å: Chain A: D.235, E.237, I.238, N.286, M.287, W.288, G.290 Chain B: V.55, T.56, R.74 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.235, A:E.237, A:N.286 Hydrogen bonds: A:D.235 Water bridges: B:R.76

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

TRS.32: 13 residues within 4Å: Chain B: F.178, P.179, A.180, V.181, S.189, L.190, S.191 Chain C: Q.154, E.155, S.156, S.170, S.171, T.172 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Q.154, C:S.156, C:S.170, C:S.170, C:T.172, C:T.172, B:P.179, B:S.189, B:S.191

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 VRC-PG04: B
Light chain of antibody VRC-PG04: 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 VRC-PG04

Light chain of antibody VRC-PG04

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