SMTL ID : 1fy6.1

AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH CADMIUM AND A5P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: P.101, A.102, K.124, R.154 Ligands: A5P.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.102 Water bridges: A:N.48, A:N.48, A:F.103, A:K.124, A:R.154, A:Q.188 Salt bridges: A:K.124, A:R.154, A:H.185 PO4.4: 4 residues within 4Å: Chain B: P.101, A.102, K.124, R.154 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:A.102 Water bridges: B:N.48, B:N.48, B:F.103, B:K.124 Salt bridges: B:K.124, B:R.154, B:H.185 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:R.49, B:S.51 Salt bridges: B:R.49, A:R.106 PO4.7: 5 residues within 4Å: Chain C: P.101, A.102, K.124, R.154 Ligands: A5P.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:A.102 Water bridges: C:N.48, C:N.48, C:F.103, C:K.124, C:R.154, C:Q.188 Salt bridges: C:K.124, C:R.154, C:H.185 PO4.10: 4 residues within 4Å: Chain D: P.101, A.102, K.124, R.154 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:A.102 Water bridges: D:N.48, D:N.48, D:F.103, D:K.124 Salt bridges: D:K.124, D:R.154, D:H.185 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:R.49, D:S.51

4 x CD: CADMIUM ION(Non-covalent)

CD.2: 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 CD.6: 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:H.185, B:E.222, B:E.222, B:D.233, H2O.8 CD.8: 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 CD.12: 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:H.185, D:E.222, D:E.222, D:D.233, H2O.19

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

A5P.3: 11 residues within 4Å: Chain A: C.11, K.46, N.48, R.49, S.50, H.185, Q.188, D.233 Chain B: R.106 Ligands: PO4.1, CD.2 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.46, A:K.46, A:N.48, A:S.50, A:S.50, A:Q.188, A:Q.188 Water bridges: A:R.49, A:S.51, A:S.54, A:K.124, A:K.124, A:Q.127, A:R.154, A:D.233, B:R.106 Salt bridges: A:R.49, B:R.106 A5P.9: 11 residues within 4Å: Chain C: C.11, K.46, N.48, R.49, S.50, H.185, Q.188, D.233 Chain D: R.106 Ligands: PO4.7, CD.8 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.46, C:K.46, C:N.48, C:S.50, C:S.50, C:Q.188, C:Q.188 Water bridges: C:R.49, C:S.51, C:S.54, C:K.124, C:K.124, C:Q.127, C:R.154, C:D.233, D:R.106 Salt bridges: C:R.49, D:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duewel, H.S. et al., Substrate and metal complexes of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Aquifex aeolicus at 1.9-A resolution. Implications for the condensation mechanism. J.Biol.Chem. (2001)

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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