SMTL ID : 1q9w.1 (2 other biounits)

S45-18 Fab pentasaccharide bisphosphate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GP1- GP4- KDO- KDO- KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose

GP1-GP4-KDO-KDO-KDO.1: 11 residues within 4Å: Chain A: N.31, R.33, S.97, Y.98, R.101 Chain B: Y.33, F.50, R.52, K.56, I.102, F.105 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.56, B:Y.33, B:Y.33, A:S.97, A:S.97, A:R.101, A:R.101 Water bridges: B:K.56, A:S.97, A:L.100 Hydrophobic interactions: B:Y.33, B:I.102 Salt bridges: B:R.52

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.102, F.103 Chain B: E.46, W.47 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: Q.6, M.21, S.22, W.41, T.107 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.22, A:T.107 MG.4: 1 residues within 4Å: Chain B: E.61 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.61, H2O.9, H2O.9, H2O.9, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, H.P. et al., Germline antibody recognition of distinct carbohydrate epitopes. Nat.Struct.Biol. (2003)

Release Date

2004-01-27

Peptides

S45-18 Fab (IgG1k) light chain: A
S45-18 Fab (IgG1k) heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

S45-18 Fab (IgG1k) light chain

S45-18 Fab (IgG1k) heavy chain

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