SMTL ID : 4hgw.1

Crystal structure of S25-2 in complex with a 5,6-dehydro-Kdo disaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

1 x KTU- KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3,5-dideoxy-alpha-D-threo-oct-5-en-2-ulopyranosidonic acid(Non-covalent)

KTU-KDO.1: 11 residues within 4Å: Chain A: N.31, Y.38, S.97, Y.98, R.101 Chain B: Y.33, F.50, R.52, N.56, H.102, E.107 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.31, A:S.97, A:S.97, A:R.101, A:R.101, B:Y.33, B:Y.33, B:N.56 Water bridges: A:R.33, B:Y.33 Hydrophobic interactions: B:Y.33 Salt bridges: B:R.52

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: E.190, R.193, H.194 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.190, A:H.194, H2O.1 ZN.3: 2 residues within 4Å: Chain A: N.143 Chain B: H.173 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.173, H2O.5, H2O.19, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brooks, C.L. et al., Exploring the cross-reactivity of S25-2: complex with a 5,6-dehydro-Kdo disaccharide. Acta Crystallogr.,Sect.F (2013)

Release Date

2013-01-09

Peptides

Antibody Fab fragment, light chain: A
Antibody Fab fragment, heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Antibody Fab fragment, light chain

Antibody Fab fragment, heavy chain

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