SMTL ID : 3e12.1

Cu2+ substituted Aquifex aeolicus KDO8PS in complex with KDO8P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x CU: COPPER (II) ION(Non-covalent)

CU.1: 5 residues within 4Å: Chain A: C.11, H.185, E.222, D.233 Ligands: KD0.3 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 CU.4: 5 residues within 4Å: Chain B: C.11, H.185, E.222, D.233 Ligands: KD0.7 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 CU.8: 5 residues within 4Å: Chain C: C.11, H.185, E.222, D.233 Ligands: KD0.10 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 CU.11: 5 residues within 4Å: Chain D: C.11, H.185, E.222, D.233 Ligands: KD0.14 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 PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: P.101, A.102, F.103, K.124, R.154 Ligands: KD0.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.102, A:F.103 Water bridges: A:Q.127 Salt bridges: A:K.124, A:R.154 PO4.5: 5 residues within 4Å: Chain B: P.101, A.102, K.124, R.154 Ligands: KD0.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.102 Water bridges: B:N.48 Salt bridges: B:K.124, B:R.154 PO4.9: 6 residues within 4Å: Chain C: P.101, A.102, F.103, K.124, R.154 Ligands: KD0.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.102, C:F.103 Water bridges: C:Q.127 Salt bridges: C:K.124, C:R.154 PO4.12: 5 residues within 4Å: Chain D: P.101, A.102, K.124, R.154 Ligands: KD0.14 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.102 Water bridges: D:N.48 Salt bridges: D:K.124, D:R.154

4 x KD0: 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid(Non-covalent)

KD0.3: 19 residues within 4Å: Chain A: C.11, K.41, S.43, K.46, N.48, R.49, S.50, D.81, Q.99, K.124, R.154, H.185, Q.188, F.220, E.222, D.233 Chain B: R.106 Ligands: CU.1, PO4.2 27 PLIP interactions: 4 interactions with chain B, 23 interactions with chain A Hydrogen bonds: B:R.106, A:S.43, A:K.46, A:N.48, A:N.48, A:N.48, A:S.50, A:R.154, A:Q.188, A:D.233 Water bridges: B:R.106, B:R.106, A:S.43, A:K.46, A:R.49, A:S.50, A:S.50, A:S.51, A:S.51, A:Q.127, A:G.192 Salt bridges: B:R.106, A:K.41, A:K.46, A:R.49, A:K.124, A:H.185 KD0.7: 18 residues within 4Å: Chain A: R.106 Chain B: C.11, K.41, S.43, K.46, N.48, R.49, S.50, D.81, Q.99, K.124, R.154, H.185, F.220, E.222, D.233 Ligands: CU.4, PO4.5 26 PLIP interactions: 23 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.43, B:K.46, B:N.48, B:N.48, B:N.48, B:S.50, B:R.154, B:D.233, B:D.233, A:R.106 Water bridges: B:S.43, B:K.46, B:R.49, B:S.50, B:S.50, B:S.51, B:S.54, B:Q.127, B:G.191, A:R.106 Salt bridges: B:K.41, B:K.46, B:R.49, B:K.124, B:H.185, A:R.106 KD0.10: 19 residues within 4Å: Chain C: C.11, K.41, S.43, K.46, N.48, R.49, S.50, D.81, Q.99, K.124, R.154, H.185, Q.188, F.220, E.222, D.233 Chain D: R.106 Ligands: CU.8, PO4.9 29 PLIP interactions: 25 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:S.43, C:K.46, C:N.48, C:N.48, C:N.48, C:S.50, C:R.154, C:Q.188, C:D.233, D:R.106 Water bridges: C:S.43, C:K.46, C:R.49, C:S.50, C:S.50, C:S.51, C:S.51, C:D.81, C:D.81, C:Q.127, C:G.192, D:R.106, D:R.106 Salt bridges: C:K.41, C:K.46, C:R.49, C:K.124, C:H.185, D:R.106 KD0.14: 18 residues within 4Å: Chain C: R.106 Chain D: C.11, K.41, S.43, K.46, N.48, R.49, S.50, D.81, Q.99, K.124, R.154, H.185, F.220, E.222, D.233 Ligands: CU.11, PO4.12 28 PLIP interactions: 25 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.43, D:K.46, D:N.48, D:N.48, D:N.48, D:S.50, D:R.154, D:D.233, D:D.233, C:R.106 Water bridges: D:S.43, D:K.46, D:R.49, D:S.50, D:S.50, D:S.51, D:S.54, D:D.81, D:D.81, D:Q.127, D:G.191, C:R.106 Salt bridges: D:K.41, D:K.46, D:R.49, D:K.124, D:H.185, C:R.106

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 2 residues within 4Å: Chain B: K.174, A.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.174 Water bridges: B:K.178 Salt bridges: B:K.174 ACT.13: 2 residues within 4Å: Chain D: K.174, A.177 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.174 Water bridges: D:K.178 Salt bridges: D:K.174

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

2009-05-12

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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