SMTL ID : 3oaz.1 (1 other biounit)

A non-self sugar mimic of the HIV glycan shield shows enhanced antigenicity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: R.72, D.73, D.74, L.75 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.73, A:D.74, A:D.74, A:L.75 Water bridges: A:D.73 GOL.2: 2 residues within 4Å: Chain A: G.200, T.201 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.203 GOL.3: 1 residues within 4Å: Chain A: K.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.216 GOL.4: 3 residues within 4Å: Chain A: N.26, F.27, R.28 No protein-ligand interaction detected (PLIP) GOL.11: 6 residues within 4Å: Chain B: E.187, K.188, H.189, K.190, R.211 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.188, B:H.189, B:R.211 GOL.12: 4 residues within 4Å: Chain A: K.139 Chain B: T.206, K.207, S.208 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:S.138, A:K.139, A:T.141, B:K.207 Hydrogen bonds: B:S.208 GOL.13: 3 residues within 4Å: Chain B: K.188, H.189 Ligands: GOL.11 No protein-ligand interaction detected (PLIP)

11 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 1 residues within 4Å: Chain A: S.101 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: D.111 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: A.92 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: N.209, K.211, K.216 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: S.122, P.123 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: S.114, N.137 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: S.142 Chain B: V.115, K.207 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: S.171 Chain B: K.169 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: P.40, A.84, T.85, R.103 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: Q.160 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain B: K.45 Ligand excluded by PLIP

1 x 2M5: methyl 7-deoxy-L-glycero-alpha-D-manno-heptopyranoside(Non-covalent)

2M5.10: 10 residues within 4Å: Chain A: A.31, H.32, T.33, K.99, G.100, L.104, S.105, D.106, N.107, D.108 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.31, A:H.32, A:T.33, A:T.33, A:D.108, A:D.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doores, K.J. et al., A nonself sugar mimic of the HIV glycan shield shows enhanced antigenicity. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2011-01-12

Peptides

Fab 2G12, heavy chain: A
Fab 2G12, light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
K

Fab 2G12, heavy chain

Fab 2G12, light chain

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