SMTL ID : 2r2b.1

Crystal structure of S25-2 Fab in complex with Kdo analogues

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x KDA- KDO- KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid

KDA-KDO-KDO.1: 13 residues within 4Å: Chain A: N.31, R.33, Y.38, S.97, Y.98, R.101 Chain B: Y.33, R.52, A.55, N.56, H.102, G.104, E.107 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.31, A:S.97, A:R.101, A:R.101, B:Y.33, B:Y.33 Water bridges: A:R.33, A:Y.38 Hydrophobic interactions: B:Y.33 Salt bridges: B:R.52

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: E.190, H.194 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.190, A:E.190, A:H.194 ZN.3: 3 residues within 4Å: Chain B: R.52, T.59, E.61 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brooks, C.L. et al., Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes. J.Mol.Biol. (2008)

Release Date

2008-12-30

Peptides

Fab, antibody fragment (IgG1k), light chain: A
Fab, antibody fragment (IgG1k), heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fab, antibody fragment (IgG1k), light chain

Fab, antibody fragment (IgG1k), heavy chain

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