SMTL ID : 4jan.1 (1 other biounit)

crystal structure of broadly neutralizing antibody CH103 in complex with HIV-1 gp120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 8 residues within 4Å: Chain A: L.145, N.146, F.243, N.244, C.245, C.308, K.309, S.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.146, A:K.309, A:K.309 NAG.2: 4 residues within 4Å: Chain A: E.159, N.160, T.162, D.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.162 NAG.3: 8 residues within 4Å: Chain A: E.203, E.204, N.207, N.259, G.260, T.261, Y.262, N.263 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.203 Hydrogen bonds: A:E.203 NAG.4: 5 residues within 4Å: Chain A: L.236, T.239, T.240, N.253, T.255 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: T.255, K.256, N.259 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.255

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

NA.6: 3 residues within 4Å: Chain B: V.92, G.114 Chain C: G.36 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.36 NA.7: 7 residues within 4Å: Chain B: K.43, G.44, L.45 Chain C: E.2, F.94, G.95, S.96 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.2

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain B: P.41 Chain C: P.7, D.80, Y.82, S.96, G.97, T.98, Q.99 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.80, C:S.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liao, H.X. et al., Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature (2013)

Release Date

2013-04-03

Peptides

ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C: A
ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103: B
ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C

ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103

ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103

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