SMTL ID : 6cxg.1

anti-HIV-1 Fab 2G12 in complex with glycopeptide 10V1S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose

BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1: 18 residues within 4Å: Chain A: G.93, Y.94 Chain B: A.31, H.32, T.33, T.53, S.54, T.56, K.99, G.100, L.104, S.105, D.106, N.107, D.108 Chain E: X.20, W.30, N.33 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.56, B:A.31, B:H.32, B:T.33, B:T.33, B:D.108, B:D.108, A:G.93 Water bridges: A:Y.94

1 x BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose

BMA-MAN-MAN-MAN-MAN-MAN-MAN.2: 17 residues within 4Å: Chain C: G.93, Y.94 Chain D: A.31, H.32, T.33, T.53, S.54, T.56, K.99, G.100, L.104, S.105, D.106, N.107, D.108 Chain F: X.20, W.30 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:Y.94, D:T.56, D:T.56

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: Q.160, S.162, S.176, S.177, T.178 Chain D: F.176, P.177, V.179, S.187, L.188, S.189 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:F.176, D:S.187, D:S.189, A:Q.160, A:S.162, A:T.178 GOL.4: 6 residues within 4Å: Chain A: T.197, H.198, L.201, S.202, S.203, P.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.198 GOL.5: 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 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Q.160, C:S.162, C:T.178, B:P.177, B:S.187, B:S.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, D.N. et al., Oligomannose Glycopeptide Conjugates Elicit Antibodies Targeting the Glycan Core Rather than Its Extremities. ACS Cent Sci (2019)

Release Date

2019-02-20

Peptides

anti-HIV-1 Fab 2G12 light chain: AC
anti-HIV-1 Fab 2g12 heavy chain: BD
10V1S glycopeptide: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
K

B
H

D
M

E
A

F
C

anti-HIV-1 Fab 2G12 light chain

anti-HIV-1 Fab 2g12 heavy chain

10V1S glycopeptide

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