SMTL ID : 4jpv.1

Crystal structure of broadly and potently neutralizing antibody 3bnc117 in complex with hiv-1 gp120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.83 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: N.118, T.120, I.156, I.161, H.220 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.161 Water bridges: A:N.118 NAG.2: 3 residues within 4Å: Chain A: H.42, N.113, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125 NAG.3: 8 residues within 4Å: Chain A: K.136, N.146, N.244, R.246, C.306, V.307, S.308 Ligands: NAG.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 Water bridges: A:V.307, A:V.307 NAG.4: 6 residues within 4Å: Chain A: E.159, N.160 Chain C: G.27, Y.28, Y.87 Ligands: NAG.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.28, C:Y.87 NAG.5: 5 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.152, A:E.153, A:E.153, A:I.154, A:N.173 NAG.6: 3 residues within 4Å: Chain A: E.177, N.179, E.200 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.179, A:Y.198, A:Y.198, A:E.200 Water bridges: A:E.177 NAG.7: 4 residues within 4Å: Chain A: N.202, T.204, K.205 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.205 NAG.8: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 Water bridges: A:N.253, A:T.255 NAG.9: 4 residues within 4Å: Chain A: N.259, T.261, C.262, G.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.261, A:G.270 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 Hydrophobic interactions: A:N.146 Hydrogen bonds: A:S.175 Water bridges: A:N.309 NAG.15: 4 residues within 4Å: Chain C: T.20, R.61, E.66, N.68 No protein-ligand interaction detected (PLIP)

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

EPE.11: 4 residues within 4Å: Chain A: L.9, A.30, Q.60, D.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.60 Salt bridges: A:D.64, A:D.64

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

EDO.12: 9 residues within 4Å: Chain A: K.91, E.248, F.249, I.281, K.282, Q.283, A.297, P.298, P.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.91, A:F.249, A:P.298 EDO.13: 4 residues within 4Å: Chain A: E.177, N.202, K.205 Ligands: NAG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.177, A:N.202 EDO.14: 6 residues within 4Å: Chain A: D.235, E.237, N.286, M.287 Chain B: K.54, T.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.237 EDO.16: 5 residues within 4Å: Chain B: Q.46, W.47 Chain C: E.88, F.89, V.90 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:W.47, C:E.88

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 STRAIN 93TH057 GP120 WITH LOOP d AND LOOPD V5 REPLACED FROM HIV STRAIN 3415V1: A
HEAVY CHAIN OF ANTIBODY 3BNC117: B
LIGHT CHAIN OF ANTIBODY 3BNC117: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

HIV-1 CLADE A STRAIN 93TH057 GP120 WITH LOOP d AND LOOPD V5 REPLACED FROM HIV STRAIN 3415V1

HEAVY CHAIN OF ANTIBODY 3BNC117

LIGHT CHAIN OF ANTIBODY 3BNC117

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