SMTL ID : 1jcx.1

Aquifex aeolicus KDO8P synthase in complex with API and Cadmium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 6 residues within 4Å: Chain A: C.11, K.46, H.185, E.222, D.233 Ligands: PAI.2 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.3: 5 residues within 4Å: Chain B: C.11, H.185, E.222, D.233 Ligands: PAI.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: 6 residues within 4Å: Chain C: C.11, K.46, H.185, E.222, D.233 Ligands: PAI.6 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.7: 5 residues within 4Å: Chain D: C.11, H.185, E.222, D.233 Ligands: PAI.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 PAI: {[(2,2-DIHYDROXY-ETHYL)-(2,3,4,5-TETRAHYDROXY-6-PHOSPHONOOXY-HEXYL)-AMINO]-METHYL}-PHOSPHONIC ACID(Non-covalent)

PAI.2: 18 residues within 4Å: Chain A: C.11, K.41, K.46, N.48, R.49, S.50, Q.99, P.101, A.102, K.124, R.154, H.185, Q.188, F.220, E.222, D.233 Chain B: R.106 Ligands: CD.1 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:K.46, A:N.48, A:N.48, A:N.48, A:S.50, A:S.50, A:Q.99, A:A.102, A:K.124, A:R.154, A:Q.188, A:E.222, A:D.233 Water bridges: A:N.48, A:S.50, A:S.51, A:S.54, A:F.103, A:Q.127, A:Q.127 Salt bridges: A:K.41, A:K.46, A:R.49, A:D.81, A:K.124, A:H.185 PAI.4: 18 residues within 4Å: Chain A: R.106 Chain B: C.11, K.41, K.46, N.48, R.49, S.50, Q.99, P.101, A.102, K.124, R.154, H.185, Q.188, F.220, E.222, D.233 Ligands: CD.3 24 PLIP interactions: 23 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.46, B:N.48, B:N.48, B:N.48, B:S.50, B:Q.99, B:A.102, B:K.124, B:R.154, B:Q.188, B:E.222, A:R.106 Water bridges: B:N.48, B:S.50, B:S.51, B:S.54, B:F.103, B:Q.127 Salt bridges: B:K.41, B:K.46, B:R.49, B:D.81, B:K.124, B:H.185 PAI.6: 18 residues within 4Å: Chain C: C.11, K.41, K.46, N.48, R.49, S.50, Q.99, P.101, A.102, K.124, R.154, H.185, Q.188, F.220, E.222, D.233 Chain D: R.106 Ligands: CD.5 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:K.46, C:N.48, C:N.48, C:N.48, C:S.50, C:S.50, C:Q.99, C:A.102, C:K.124, C:R.154, C:Q.188, C:E.222, C:D.233 Water bridges: C:N.48, C:S.50, C:S.51, C:S.54, C:D.81, C:F.103, C:Q.127 Salt bridges: C:K.41, C:K.46, C:R.49, C:D.81, C:K.124, C:H.185 PAI.8: 18 residues within 4Å: Chain C: R.106 Chain D: C.11, K.41, K.46, N.48, R.49, S.50, Q.99, P.101, A.102, K.124, R.154, H.185, Q.188, F.220, E.222, D.233 Ligands: CD.7 25 PLIP interactions: 24 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.46, D:N.48, D:N.48, D:N.48, D:S.50, D:Q.99, D:A.102, D:K.124, D:R.154, D:Q.188, D:E.222, C:R.106 Water bridges: D:N.48, D:S.50, D:S.51, D:S.54, D:D.81, D:F.103, D:Q.127 Salt bridges: D:K.41, D:K.46, D:R.49, D:D.81, D:K.124, D:H.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis. Biochemistry (2001)

Release Date

2002-01-16

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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