SMTL ID : 4jpw.1

Crystal structure of broadly and potently neutralizing antibody 12a21 in complex with hiv-1 strain 93th057 gp120 mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: N.118, G.121, P.122, I.156, S.158, L.161, H.220 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118 Water bridges: A:N.118, A:N.118 NAG.2: 5 residues within 4Å: Chain A: E.40, H.42, N.113, N.125, S.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40, A:E.40 NAG.3: 11 residues within 4Å: Chain A: D.95, K.136, V.138, N.146, F.243, N.244, R.246, C.306, V.307, S.308 Ligands: NAG.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.243 Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:R.246, A:S.308 NAG.4: 8 residues within 4Å: Chain A: E.159, N.160, T.162 Chain C: G.28, I.29, S.32, V.90, F.91 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.29, C:V.90, C:F.91 Hydrogen bonds: C:G.28, C:S.32, C:S.32, A:N.160 Water bridges: C:G.30, C:S.31, C:S.31 NAG.5: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.154, A:N.173 NAG.6: 3 residues within 4Å: Chain A: N.179, T.181, E.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.179, A:T.181 Water bridges: A:E.200 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: N.253, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.253 NAG.9: 7 residues within 4Å: Chain A: Q.256, N.259, T.261, C.262, M.268, K.269, C.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.259, A:K.269 NAG.10: 4 residues within 4Å: Chain A: N.146, S.175, N.309 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.175 Water bridges: A:E.177, A:E.177

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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.283, A:I.284 Salt bridges: A:K.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klein, F. et al., Somatic mutations of the immunoglobulin framework are generally required for broad and potent HIV-1 neutralization. Cell(Cambridge,Mass.) (2013)

Release Date

2013-04-17

Peptides

HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375S: A
HEAVY CHAIN OF ANTIBODY 12A21: B
LIGHT CHAIN OF ANTIBODY 12A21: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375S

HEAVY CHAIN OF ANTIBODY 12A21

LIGHT CHAIN OF ANTIBODY 12A21

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