SMTL ID : 1pck.1

Aquifex aeolicus KDO8PS in complex with Z-methyl-PEP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.50 Water bridges: A:R.49, 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: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.50 Water bridges: B:S.50, B:S.51, B:S.54, B:G.191 Salt bridges: B:R.49, A:R.106 PO4.7: 3 residues within 4Å: Chain C: R.49, S.50 Chain D: R.106 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.50 Water bridges: C:R.49, 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: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.50 Water bridges: D:S.50, D:S.51, D:S.54, D:G.191 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, H.185, E.222, D.233 Ligands: PEZ.3 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.6 CD.5: 6 residues within 4Å: Chain B: C.11, K.46, H.185, E.222, D.233 Ligands: PEZ.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 CD.8: 5 residues within 4Å: Chain C: C.11, H.185, E.222, D.233 Ligands: PEZ.9 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.17 CD.11: 6 residues within 4Å: Chain D: C.11, K.46, H.185, E.222, D.233 Ligands: PEZ.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 PEZ: 2-(PHOSPHONOOXY)BUTANOIC ACID(Non-covalent)

PEZ.3: 13 residues within 4Å: Chain A: K.41, S.43, K.46, N.48, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220 Ligands: CD.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.43, A:D.81, A:A.102 Water bridges: A:N.48, A:F.103, A:R.154, 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 PEZ.6: 14 residues within 4Å: Chain B: K.41, S.43, K.46, N.48, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220, E.222 Ligands: CD.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.43, B:S.43, B:A.102 Water bridges: 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 PEZ.9: 13 residues within 4Å: Chain C: K.41, S.43, K.46, N.48, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220 Ligands: CD.8 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.43, C:D.81, C:A.102 Water bridges: C:N.48, C:D.81, C:F.103, C:R.154, 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 PEZ.12: 14 residues within 4Å: Chain D: K.41, S.43, K.46, N.48, D.81, Q.99, P.101, A.102, K.124, R.154, H.185, F.220, E.222 Ligands: CD.11 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.43, D:S.43, D:A.102 Water bridges: 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

Xu, X. et al., Structure-Based Design of Novel Inhibitors of 3-Deoxy-D-manno-octulosonate 8-Phosphate Synthase. DRUG DES.DISCOVERY (2003)

Release Date

2004-02-17

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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