SMTL ID : 4xvt.1

Crystal structure of HIV-1 93TH057 coreE gp120 with antibody 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: T.120, E.159, N.160 Chain C: Y.28, G.29, S.30 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:T.120, A:E.159 Hydrogen bonds: A:E.159, A:N.160, C:Y.28, C:S.30 Water bridges: A:E.159, A:N.160, C:Y.89, C:Y.89 NAG.2: 6 residues within 4Å: Chain A: N.118, T.120, I.156, S.158, L.161, H.220 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118, A:T.120 Water bridges: A:N.118, A:N.118, A:S.158 NAG.3: 2 residues within 4Å: Chain A: E.44, N.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.44, A:N.45 NAG.4: 2 residues within 4Å: Chain A: N.113, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125 NAG.5: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.153, A:I.154, A:Q.212 NAG.6: 9 residues within 4Å: Chain A: D.95, P.96, K.136, L.145, N.146, N.244, C.306, V.307, S.308 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:S.308 Water bridges: A:D.95 NAG.7: 4 residues within 4Å: Chain A: N.179, T.181, E.200, V.307 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.307 Hydrogen bonds: A:N.179, A:E.200 Water bridges: A:N.179 NAG.8: 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.9: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.253 Water bridges: A:N.253, A:T.255 NAG.10: 6 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261, C.262, C.271 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.255 Water bridges: A:N.259, A:N.272 NAG.11: 5 residues within 4Å: Chain A: N.322, N.323 Chain C: V.3, L.4, F.92 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.3, C:L.4, C:L.4

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 (2015)

Release Date

2015-07-15

Peptides

ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE A/E: A
donor 45 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Heavy chain: B
45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE A/E

donor 45 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Heavy chain

45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Light chain

Related Entries With Identical Sequence