SMTL ID : 1fws.1

AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH PEP AND CADMIUM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: R.49, S.50 Chain B: R.106 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.50 Water bridges: A:S.51, A:S.54 Salt bridges: A:R.49, B:R.106 PO4.4: 3 residues within 4Å: Chain A: R.106 Chain B: R.49, S.50 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Water bridges: A:R.106, A:R.106, B:R.49, B:S.51 Salt bridges: A:R.106, B:R.49 Hydrogen bonds: B:S.50 PO4.7: 3 residues within 4Å: Chain C: R.49, S.50 Chain D: R.106 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.50 Water bridges: C:S.51, C:S.54 Salt bridges: C:R.49, D:R.106 PO4.10: 3 residues within 4Å: Chain C: R.106 Chain D: R.49, S.50 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.50 Water bridges: D:R.49, D:S.51, C:R.106, C:R.106 Salt bridges: D:R.49, C:R.106

4 x CD: CADMIUM ION(Non-covalent)

CD.2: 5 residues within 4Å: Chain A: C.11, K.46, H.185, E.222, D.233 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.11, A:H.185, A:E.222, A:D.233, H2O.3 CD.5: 4 residues within 4Å: Chain B: C.11, H.185, E.222, D.233 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.11, B:H.185, B:E.222, B:D.233, H2O.10 CD.8: 5 residues within 4Å: Chain C: C.11, K.46, H.185, E.222, D.233 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.11, C:H.185, C:E.222, C:D.233, H2O.15 CD.11: 4 residues within 4Å: Chain D: C.11, H.185, E.222, D.233 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.11, D:H.185, D:E.222, D:D.233, H2O.21

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.3: 12 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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.43, A:A.102 Water bridges: A:N.48, A:N.48, 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.6: 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, E.222 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.43, B:A.102 Water bridges: B:N.48, B:N.48, B:F.103, B:R.154 Salt bridges: B:K.41, B:K.46, B:K.124, B:K.124, B:R.154, B:H.185, B:H.185 PEP.9: 12 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 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.43, C:A.102 Water bridges: C:N.48, C:N.48, C:D.81, 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.12: 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, E.222 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.43, D:A.102 Water bridges: D:N.48, D:N.48, D:D.81, D:F.103, D:R.154 Salt bridges: D:K.41, D:K.46, D:K.124, D:K.124, D:R.154, D:H.185, D:H.185

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

2001-04-21

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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