SMTL ID : 3hzy.1

Crystal structure of S73-2 antibody in complex with antigen Kdo(2.4)Kdo(2.4)Kdo

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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: 12 residues within 4Å: Chain A: N.31, R.33, Y.38, S.97, Y.98, R.101 Chain B: Y.33, R.52, K.56, I.102, P.104, D.111 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.31, A:R.33, A:R.33, B:Y.33, B:Y.33, A:S.97, A:Y.98, A:R.101, A:R.101 Salt bridges: A:R.33, B:R.52 Hydrophobic interactions: B:I.102 Water bridges: A:Y.38, A:L.100

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: N.143, D.172, D.175, T.177 Chain B: H.177 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.177 MG.7: 4 residues within 4Å: Chain A: E.61 Chain B: Y.110, D.114 Ligands: ZN.4 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.61, B:Y.110, H2O.3

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: D.156, R.193, H.194 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.156, A:H.194, H2O.3 ZN.4: 3 residues within 4Å: Chain A: E.61 Chain B: Y.110 Ligands: MG.7 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.61, B:Y.110, H2O.1, H2O.3 ZN.5: 3 residues within 4Å: Chain A: R.160, E.190, H.194 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.190, A:H.194, H2O.3 ZN.6: 1 residues within 4Å: Chain B: E.61 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brooks, C.L. et al., Antibodies raised against chlamydial lipopolysaccharide antigens reveal convergence in germline gene usage and differential epitope recognition. Biochemistry (2010)

Release Date

2010-01-12

Peptides

S73-2 Fab (IgG1k) light chain: A
S73-2 Fab (IgG1k) heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

S73-2 Fab (IgG1k) light chain

S73-2 Fab (IgG1k) heavy chain