SMTL ID : 4rbp.1

Crystal structure of HIV neutralizing antibody 2G12 in complex with a bacterial oligosaccharide analog of mammalian oligomanose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-2-2-mer

Ligands

2 x KDO- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-5)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid(Non-functional Binders)

KDO-MAN-MAN-MAN-MAN-MAN.1: 15 residues within 4Å: Chain A: G.93, Y.94 Chain B: A.31, H.32, T.33, T.53, Y.57, K.99, G.100, L.104, S.105, D.106, N.107, D.108 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.106 KDO-MAN-MAN-MAN-MAN-MAN.2: 12 residues within 4Å: Chain C: G.93, Y.94 Chain D: A.31, H.32, T.33, K.99, G.100, L.104, S.105, D.106, N.107, D.108 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.106

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: P.113, S.114, V.115, F.116, V.205, K.207 Chain D: S.142 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:S.142, A:P.113, A:V.115, A:K.207, A:K.207 Water bridges: D:S.142, D:S.142 GOL.4: 5 residues within 4Å: Chain A: R.108, T.109, K.169, D.170, S.171 No protein-ligand interaction detected (PLIP) GOL.5: 2 residues within 4Å: Chain B: R.87, E.89 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.87 GOL.6: 5 residues within 4Å: Chain B: L.75, E.76 Chain D: S.55, T.56, R.58 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:R.58, B:E.76 Water bridges: B:L.75, B:L.75 GOL.7: 2 residues within 4Å: Chain B: A.31 Ligands: KDO-MAN-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain C: E.30, T.31, W.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.31 GOL.9: 11 residues within 4Å: Chain B: F.176, P.177, V.179, S.187, L.188, S.189 Chain C: Q.160, S.162, S.176, S.177, T.178 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.162, C:S.176, C:S.177, B:P.177, B:S.189 Water bridges: C:T.178, C:T.178 GOL.10: 9 residues within 4Å: Chain C: Q.37, K.45, L.47, G.57, V.58, P.59, R.61, F.62, D.81 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.37, C:D.81 Water bridges: C:K.39, C:D.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stanfield, R.L. et al., Crystal structure of the HIV neutralizing antibody 2G12 in complex with a bacterial oligosaccharide analog of mammalian oligomannose. Glycobiology (2015)

Release Date

2014-11-26

Peptides

Fab 2G12 light chain: AC
Fab 2G12 heavy chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
K

B
H

D
M

Fab 2G12 light chain

Fab 2G12 heavy chain

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