SMTL ID : 2a2i.1

Aquifex aeolicus KDO8PS in complex with PEP, A5P, Zn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.11, K.46, H.185, E.222, D.233 Ligands: A5P.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.11, A:H.185, A:E.222, A:E.222, A:D.233 ZN.4: 5 residues within 4Å: Chain B: C.11, H.185, E.222, D.233 Ligands: A5P.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.11, B:H.185, B:E.222, B:E.222, B:D.233 ZN.7: 6 residues within 4Å: Chain C: C.11, K.46, H.185, E.222, D.233 Ligands: A5P.9 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.11, C:H.185, C:E.222, C:E.222, C:D.233 ZN.10: 5 residues within 4Å: Chain D: C.11, H.185, E.222, D.233 Ligands: A5P.12 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.11, D:H.185, D:E.222, D:E.222, D:D.233

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 13 residues within 4Å: Chain A: K.41, S.43, K.46, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220, E.222 Ligands: A5P.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.43, A:A.102 Water bridges: A:F.103, A:R.154 Salt bridges: A:K.41, A:K.46, A:K.124, A:K.124, A:R.154, A:H.185, A:H.185 PEP.5: 12 residues within 4Å: Chain B: K.41, S.43, K.46, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220 Ligands: A5P.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.43, B:A.102 Water bridges: B:F.103 Salt bridges: B:K.41, B:K.46, B:K.124, B:K.124, B:R.154, B:H.185, B:H.185 PEP.8: 13 residues within 4Å: Chain C: K.41, S.43, K.46, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220, E.222 Ligands: A5P.9 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.43, C:A.102 Water bridges: C:D.81, C:D.81, C:F.103, C:R.154 Salt bridges: C:K.41, C:K.46, C:K.124, C:K.124, C:R.154, C:H.185, C:H.185 PEP.11: 12 residues within 4Å: Chain D: K.41, S.43, K.46, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220 Ligands: A5P.12 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.43, D:A.102 Water bridges: D:D.81, D:F.103 Salt bridges: D:K.41, D:K.46, D:K.124, D:K.124, D:R.154, D:H.185, D:H.185

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

A5P.3: 13 residues within 4Å: Chain A: K.46, N.48, R.49, S.50, R.154, H.185, Q.188, K.196, S.197, D.233 Chain B: R.106 Ligands: ZN.1, PEP.2 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.46, A:K.46, A:N.48, A:S.50, A:S.50, A:R.154, A:Q.188, A:Q.188, A:S.197, A:D.233 Water bridges: A:R.49, A:Q.127, A:Q.127 Salt bridges: A:R.49, B:R.106 A5P.6: 12 residues within 4Å: Chain A: R.106 Chain B: C.11, K.46, N.48, R.49, S.50, H.185, Q.188, S.232, D.233 Ligands: ZN.4, PEP.5 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.46, B:K.46, B:N.48, B:S.50, B:Q.188 Water bridges: B:S.54, B:S.54, B:Q.127, B:R.154, A:R.106, A:R.106 Salt bridges: B:R.49, A:R.106 A5P.9: 13 residues within 4Å: Chain C: K.46, N.48, R.49, S.50, R.154, H.185, Q.188, K.196, S.197, D.233 Chain D: R.106 Ligands: ZN.7, PEP.8 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.46, C:K.46, C:N.48, C:S.50, C:S.50, C:R.154, C:Q.188, C:Q.188, C:S.197, C:D.233 Water bridges: C:R.49, C:Q.127, C:Q.127 Salt bridges: C:R.49, D:R.106 A5P.12: 12 residues within 4Å: Chain C: R.106 Chain D: C.11, K.46, N.48, R.49, S.50, H.185, Q.188, S.232, D.233 Ligands: ZN.10, PEP.11 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:K.46, D:K.46, D:N.48, D:S.50, D:Q.188 Water bridges: D:S.54, D:S.54, D:Q.127, D:R.154, C:R.106, C:R.106 Salt bridges: D:R.49, C:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kona, F. et al., Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis. Biochemistry (2009)

Release Date

2006-07-04

Peptides

2-dehydro-3-deoxyphosphooctonate aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

2-dehydro-3-deoxyphosphooctonate aldolase

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