SMTL ID : 4lss.1

Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 clade A strain KER_2018_11 gp120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.45 NAG.2: 5 residues within 4Å: Chain A: N.118, T.120, G.121, I.156, H.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.220 Water bridges: A:S.158 NAG.3: 4 residues within 4Å: Chain A: H.42, K.113, E.115, N.125 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.125 Hydrogen bonds: A:H.42 NAG.4: 10 residues within 4Å: Chain A: E.95, P.96, K.136, V.138, L.145, N.146, C.309, Q.310, S.311 Ligands: NAG.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:E.95, A:K.136, A:N.146, A:S.311 NAG.5: 4 residues within 4Å: Chain A: N.51, E.159, N.160 Chain C: Y.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.51, A:E.159 Water bridges: A:N.160 NAG.6: 3 residues within 4Å: Chain A: N.202, D.276, N.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.202 NAG.7: 1 residues within 4Å: Chain A: N.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.207 Water bridges: A:N.207, A:N.207 NAG.8: 1 residues within 4Å: Chain A: N.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.222 NAG.9: 4 residues within 4Å: Chain A: T.238, T.239, N.252, S.254 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.239 Hydrogen bonds: A:N.252, A:S.254 Water bridges: A:E.229, A:S.254 NAG.10: 2 residues within 4Å: Chain A: N.258, S.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.258 Water bridges: A:T.260 NAG.11: 4 residues within 4Å: Chain A: N.146, P.175, N.312 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.312 NAG.12: 5 residues within 4Å: Chain A: T.224, I.226, N.262, T.331, N.332 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.224 Hydrogen bonds: A:T.224, A:N.332

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.13: 6 residues within 4Å: Chain A: L.9, C.11, H.29, A.30, Q.60, D.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.9 Salt bridges: A:D.64, A:D.64 EPE.17: 2 residues within 4Å: Chain B: G.142, T.143 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.142, B:T.143, B:T.143

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.14: 4 residues within 4Å: Chain A: V.139, S.241, F.242, F.248 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.139 Water bridges: A:N.289

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

NA.15: 3 residues within 4Å: Chain A: K.19, T.20, E.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.20, A:E.21 NA.16: 4 residues within 4Å: Chain A: K.74, P.75, Q.87, A.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.87, A:A.88 NA.18: 5 residues within 4Å: Chain B: Y.104, W.106 Chain C: S.30, Q.88, Y.89 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.30, C:Y.89, B:Y.104

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: A
HEAVY CHAIN OF ANTIBODY VRC01: B
LIGHT CHAIN OF ANTIBODY VRC01 with N72T mutation: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

envelope glycoprotein GP120

HEAVY CHAIN OF ANTIBODY VRC01

LIGHT CHAIN OF ANTIBODY VRC01 with N72T mutation

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