SMTL ID : 1pcw.1

Aquifex aeolicus KDO8PS in complex with cadmium and APP, a bisubstrate inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 5 residues within 4Å: Chain A: C.11, H.185, E.222, D.233 Ligands: H4P.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.2: 5 residues within 4Å: Chain B: C.11, H.185, E.222, D.233 Ligands: H4P.4 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.5: 5 residues within 4Å: Chain C: C.11, H.185, E.222, D.233 Ligands: H4P.7 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.6: 5 residues within 4Å: Chain D: C.11, H.185, E.222, D.233 Ligands: H4P.8 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 H4P: 1-DEOXY-6-O-PHOSPHONO-1-[(PHOSPHONOMETHYL)AMINO]-L-THREO-HEXITOL(Non-covalent)

H4P.3: 14 residues within 4Å: Chain A: C.11, K.46, N.48, R.49, S.50, P.101, A.102, K.124, R.154, H.185, Q.188, D.233 Chain B: R.106 Ligands: CD.1 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.46, A:N.48, A:S.50, A:S.50, A:A.102, A:K.124, A:R.154, A:Q.188, A:Q.188 Water bridges: A:K.41, A:N.48, A:R.49, A:S.51, A:S.54, A:F.103, A:K.124, A:Q.127, A:G.191, A:D.233, B:R.106 Salt bridges: A:R.49, B:R.106 H4P.4: 13 residues within 4Å: Chain A: R.106 Chain B: C.11, K.46, N.48, R.49, S.50, P.101, A.102, K.124, R.154, H.185, D.233 Ligands: CD.2 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.46, B:K.46, B:N.48, B:S.50, B:A.102, B:K.124, B:R.154, A:R.106 Water bridges: B:K.41, B:S.43, B:N.48, B:S.51, B:S.54, B:F.103, B:Q.127 Salt bridges: B:R.49, A:R.106 H4P.7: 14 residues within 4Å: Chain C: C.11, K.46, N.48, R.49, S.50, P.101, A.102, K.124, R.154, H.185, Q.188, D.233 Chain D: R.106 Ligands: CD.5 23 PLIP interactions: 21 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.46, C:N.48, C:S.50, C:S.50, C:A.102, C:K.124, C:R.154, C:Q.188, C:Q.188 Water bridges: C:K.41, C:N.48, C:R.49, C:S.51, C:S.54, C:D.81, C:F.103, C:K.124, C:Q.127, C:G.191, C:D.233, D:R.106 Salt bridges: C:R.49, D:R.106 H4P.8: 13 residues within 4Å: Chain C: R.106 Chain D: C.11, K.46, N.48, R.49, S.50, P.101, A.102, K.124, R.154, H.185, D.233 Ligands: CD.6 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.46, D:K.46, D:N.48, D:S.50, D:A.102, D:K.124, D:R.154, C:R.106 Water bridges: D:K.41, D:S.43, D:N.48, D:S.51, D:S.54, D:D.81, D:F.103, D:Q.127 Salt bridges: D:R.49, C:R.106

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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