SMTL ID : 4lsu.1

Crystal structure of broadly and potently neutralizing antibody VRC-PG20 in complex with HIV-1 clade A/E 93TH057 gp120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.118, T.120, I.156, S.158, H.220 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.120, A:T.120 NAG.2: 3 residues within 4Å: Chain A: N.113, K.115, N.125 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.40, A:N.113, A:K.115, A:N.125 NAG.3: 12 residues within 4Å: Chain A: D.95, P.96, K.136, V.138, L.145, N.146, N.244, R.246, C.306, V.307, S.308 Ligands: NAG.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 NAG.4: 5 residues within 4Å: Chain A: N.160, T.162 Chain B: R.105 Chain C: S.26, T.27 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:T.162, C:T.27, B:R.105 NAG.5: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.208, Q.212, K.216 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.154, A:Q.212 Hydrogen bonds: A:E.153, A:I.154, A:N.173, A:K.208, A:K.208, A:Q.212 Water bridges: A:K.174 NAG.6: 2 residues within 4Å: Chain A: N.179, E.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.179, A:E.200 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.202, A:K.205 NAG.8: 2 residues within 4Å: Chain A: N.222, N.223 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.222 Hydrogen bonds: A:N.223 NAG.9: 2 residues within 4Å: Chain A: N.253, T.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.255 Water bridges: A:N.253 NAG.10: 4 residues within 4Å: Chain A: N.146, S.175, N.309 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175, A:N.309

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

EPE.11: 5 residues within 4Å: Chain A: R.195, I.281, K.282, Q.283, I.284 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.195, A:Q.283, A:I.284 Salt bridges: A:K.282

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

EDO.12: 9 residues within 4Å: Chain A: A.165, K.166, T.167, T.316, G.333, G.334 Chain B: F.33, W.50, Q.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.165, A:T.316, A:G.334 EDO.13: 8 residues within 4Å: Chain A: S.140, L.314, G.333, G.334, N.335, I.336, N.339 Chain B: W.55 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.140, A:G.334 Water bridges: A:G.333, A:G.333, A:G.333 EDO.14: 4 residues within 4Å: Chain B: Q.1, V.2, Q.110, H.111 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.2 Water bridges: B:R.98, B:R.98, B:H.111 EDO.15: 4 residues within 4Å: Chain B: Q.110, H.111, W.112 Chain C: A.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.110, B:W.112 EDO.17: 8 residues within 4Å: Chain B: Q.39, P.41, G.42 Chain C: Q.34, Y.35, A.36, D.37, Y.81 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.37, B:G.42 Water bridges: C:Q.34, C:Q.34, C:D.37, C:D.37, C:K.38, B:G.42

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

CL.16: 1 residues within 4Å: Chain B: K.219 Ligand excluded by PLIP

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

HIV-1 CLADE A/E STRAIN 93TH057 GP120: A
HEAVY CHAIN OF ANTIBODY VRC-PG20: B
LIGHT CHAIN OF ANTIBODY VRC-PG20: 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-PG20

LIGHT CHAIN OF ANTIBODY VRC-PG20

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