SMTL ID : 4lsq.1

Crystal structure of broadly and potently neutralizing antibody VRC-CH31 in complex with HIV-1 clade A/E gp120 93TH057 with LOOP D and Loop V5 from clade A strain 3415_v1_c1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.118, T.120, G.121, I.161, H.220 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.161 Hydrogen bonds: A:N.118, A:H.220 Water bridges: A:N.118 NAG.2: 4 residues within 4Å: Chain A: E.40, H.42, N.113, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.42 Water bridges: A:K.115 NAG.3: 11 residues within 4Å: Chain A: P.96, K.136, V.138, L.145, N.146, F.243, N.244, R.246, C.306, V.307, S.308 7 PLIP interactions: 7 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 NAG.4: 8 residues within 4Å: Chain A: E.159, N.160, T.162 Chain C: 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:T.162, C:I.29, C:D.32, C:D.32, C:Q.90, C:Y.91 Water bridges: A:N.160 NAG.5: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, Q.212, K.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.154, A:N.173, A:K.216 Water bridges: A:Q.212, A:Q.212 NAG.6: 7 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200, K.303, N.305, V.307 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.179, A:T.181, A:Y.198, A:Y.198, A:E.200, A:K.303 Water bridges: A:N.305 NAG.7: 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.8: 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.255, A:T.255 NAG.9: 8 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261, C.262, M.268, K.269, C.271 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.268 Water bridges: A:N.259, A:N.259, A:C.262

5 x CD: CADMIUM ION(Non-covalent)

CD.10: 2 residues within 4Å: Chain A: H.100, G.134 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.100, H2O.1, H2O.2 CD.11: 1 residues within 4Å: Chain A: D.64 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.64, H2O.7, H2O.7 CD.18: 5 residues within 4Å: Chain B: H.41, F.42, E.115 Ligands: CL.20, CL.21 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.41, B:E.115, H2O.11 CD.19: 3 residues within 4Å: Chain B: G.180, H.182 Chain C: N.134 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.182, H2O.15, H2O.15 CD.22: 1 residues within 4Å: Chain C: H.185 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.185, H2O.13, H2O.15, H2O.15, H2O.15

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

BU3.12: 14 residues within 4Å: Chain A: T.141, E.237, I.238, H.242, N.286, M.287, W.288, G.290, G.333, N.334, I.335 Chain B: T.63, N.64 Ligands: NA.15 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.63, B:N.64, A:G.333 Hydrophobic interactions: A:E.237

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

CL.13: 4 residues within 4Å: Chain A: R.195, K.282, Q.283, I.284 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: P.39, E.40, H.41 Ligands: CD.18, CL.21 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: F.42, E.115 Ligands: CD.18, CL.20 Ligand excluded by PLIP

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

NA.14: 5 residues within 4Å: Chain A: S.232, D.318, R.329 Chain B: Y.69, W.71 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.318, A:R.329, B:Y.69 Water bridges: A:S.232 NA.15: 7 residues within 4Å: Chain A: D.235, N.286 Chain B: T.63, N.64, R.81, M.85 Ligands: BU3.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.235, B:T.63 Water bridges: A:N.286 NA.16: 5 residues within 4Å: Chain A: P.230, P.231, N.253, T.254, T.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 Water bridges: A:T.254 NA.17: 6 residues within 4Å: Chain A: K.91, I.92, R.246, G.247, E.248, I.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.246, A:E.248 Water bridges: A:I.92

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

2013-08-21

Peptides

ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN 3415_V1_C1: A
HEAVY CHAIN OF ANTIBODY VRC-CH31: B
LIGHT CHAIN OF ANTIBODY VRC-CH31 WITH N70D MUTATION: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN 3415_V1_C1

HEAVY CHAIN OF ANTIBODY VRC-CH31

LIGHT CHAIN OF ANTIBODY VRC-CH31 WITH N70D MUTATION

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