SMTL ID : 4s1s.1

Crystal structure of a VRC01-lineage antibody, 45-VRC01.H5.F-185917, in complex with clade A/E HIV-1 gp120 core

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.39 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, S.158, L.161, H.220 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118 NAG.2: 4 residues within 4Å: Chain A: H.42, N.113, K.115, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.42 NAG.3: 10 residues within 4Å: Chain A: D.95, P.96, V.138, N.146, N.244, R.246, C.306, V.307, S.308 Ligands: NAG.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.138 Hydrogen bonds: A:R.246, A:S.308, A:S.308 NAG.4: 3 residues within 4Å: Chain A: N.160, T.162 Chain C: Y.89 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.162 Hydrogen bonds: A:T.162 NAG.5: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.154 NAG.6: 4 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.179, A:T.181, A:Y.198 NAG.7: 4 residues within 4Å: Chain A: N.202, T.204, K.205, T.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.202 NAG.8: 3 residues within 4Å: Chain A: T.239, N.253, T.255 No protein-ligand interaction detected (PLIP) NAG.9: 6 residues within 4Å: Chain A: T.255, Q.256, N.259, C.262, G.270, C.271 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.256 NAG.10: 4 residues within 4Å: Chain A: N.146, S.175, N.309 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.175

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

EPE.11: 7 residues within 4Å: Chain A: L.9, C.11, H.29, A.30, Q.60, D.64, Y.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.9, A:Q.60 Salt bridges: A:D.64, A:D.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, X. et al., Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Cell(Cambridge,Mass.) (2015)

Release Date

2015-04-22

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
Fab of VRC01-lineage antibody,45-VRC01.H5.F-185917 heavy chain: B
Fab of VRC01 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

clade A/E 93TH057 HIV-1 gp120 core

Fab of VRC01-lineage antibody,45-VRC01.H5.F-185917 heavy chain

Fab of VRC01 light chain

Related Entries With Identical Sequence