SMTL ID : 1lrq.1

Aquifex aeolicus KDO8P synthase H185G mutant in complex with PEP, A5P and Cadmium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 5 residues within 4Å: Chain A: C.11, E.222, D.233 Ligands: PEP.2, A5P.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.11, A:E.222, A:E.222, A:D.233 CD.6: 4 residues within 4Å: Chain B: C.11, K.46, E.222, D.233 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.11, B:E.222, B:E.222, B:D.233, H2O.10 CD.7: 5 residues within 4Å: Chain C: C.11, E.222, D.233 Ligands: PEP.8, A5P.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.11, C:E.222, C:E.222, C:D.233 CD.12: 4 residues within 4Å: Chain D: C.11, K.46, E.222, D.233 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.11, D:E.222, D:E.222, D:D.233, H2O.20

2 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 11 residues within 4Å: Chain A: C.11, K.46, D.81, P.101, A.102, K.124, R.154, E.222, D.233 Ligands: CD.1, A5P.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:A.102, A:R.154 Water bridges: A:K.41, A:K.41, A:S.43, A:N.48, A:F.103, A:K.124, A:D.182 Salt bridges: A:K.41, A:K.46, A:K.124, A:K.124, A:R.154 PEP.8: 11 residues within 4Å: Chain C: C.11, K.46, D.81, P.101, A.102, K.124, R.154, E.222, D.233 Ligands: CD.7, A5P.9 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:A.102, C:R.154 Water bridges: C:K.41, C:K.41, C:S.43, C:N.48, C:F.103, C:K.124, C:D.182 Salt bridges: C:K.41, C:K.46, C:K.124, C:K.124, C:R.154

2 x A5P: ARABINOSE-5-PHOSPHATE(Non-covalent)

A5P.3: 11 residues within 4Å: Chain A: K.46, N.48, R.49, S.50, R.154, Q.188, K.196, S.197, D.233 Ligands: CD.1, PEP.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.46, A:K.46, A:N.48, A:S.50, A:S.50, A:R.154, A:Q.188, A:S.197, A:D.233 Water bridges: A:S.51, A:S.54, A:Q.127, A:Q.127 Salt bridges: A:R.49 A5P.9: 11 residues within 4Å: Chain C: K.46, N.48, R.49, S.50, R.154, Q.188, K.196, S.197, D.233 Ligands: CD.7, PEP.8 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:K.46, C:K.46, C:N.48, C:S.50, C:S.50, C:R.154, C:Q.188, C:S.197, C:D.233 Water bridges: C:S.51, C:S.54, C:Q.127, C:Q.127 Salt bridges: C:R.49

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain B: P.101, A.102, K.124, R.154 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.102 Water bridges: B:K.46, B:K.46, B:N.48, B:N.48, B:D.81, B:F.103, B:K.124 Salt bridges: B:K.124, B:R.154 PO4.5: 3 residues within 4Å: Chain A: R.106 Chain B: R.49, S.50 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.50 Water bridges: B:S.51, B:S.54 Salt bridges: B:R.49, A:R.106 PO4.10: 4 residues within 4Å: Chain D: P.101, A.102, K.124, R.154 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:A.102 Water bridges: D:K.46, D:K.46, D:N.48, D:N.48, D:D.81, D:F.103, D:K.124 Salt bridges: D:K.124, D:R.154 PO4.11: 3 residues within 4Å: Chain C: R.106 Chain D: R.49, S.50 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Salt bridges: C:R.106, D:R.49 Hydrogen bonds: D:S.50 Water bridges: D:S.51, D:S.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Function of His185 in Aquifex aeolicus 3-Deoxy-D-manno-octulosonate 8-Phosphate Synthase. J.Mol.Biol. (2002)

Release Date

2002-11-27

Peptides

KDO-8-phosphate synthetase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

KDO-8-phosphate synthetase

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