SMTL ID : 3fyp.1

Crystal structure of the quadruple mutant (N23C/C246S/D247E/P249A) of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: H.37, H.255, L.256, L.257, E.258 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain D: K.52, Q.110, K.135, H.199, F.234 Ligands: PEP.5 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain B: G.21, I.22, C.23, K.52, K.57, E.236, S.237 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.21, B:K.52, B:K.52, B:K.57, B:K.57 Water bridges: B:G.21 GOL.3: 6 residues within 4Å: Chain B: K.82, A.103, E.104, V.105, D.107, N.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.82, B:A.103, B:D.107 Water bridges: B:D.107

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain C: A.103, C.106, D.107, N.130 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:C.106, C:N.130 NA.7: 5 residues within 4Å: Chain A: F.169 Chain B: S.168 Chain D: S.168, F.169, G.170 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.170, D:G.170

1 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.5: 12 residues within 4Å: Chain D: K.52, S.54, K.57, Q.110, P.112, A.113, K.135, R.165, H.199, F.234, E.236 Ligands: CL.6 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:S.54, D:Q.110, D:A.113, D:E.236 Water bridges: D:S.54, D:K.57, D:F.114, D:K.135, D:K.135 Salt bridges: D:K.52, D:K.57, D:K.135, D:K.135, D:R.165, D:H.199, D:H.199

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.8: 3 residues within 4Å: Chain D: C.23, H.199, E.236 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.199, D:E.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cochrane, F.C. et al., Reversing evolution: re-establishing obligate metal ion dependence in a metal-independent KDO8P synthase. J.Mol.Biol. (2009)

Release Date

2009-03-31

Peptides

3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase