- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CU: COPPER (II) ION(Non-covalent)
- 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
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CU: COPPER (II) ION(Non-covalent)
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x KD0: 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid(Non-covalent)
- 2 x ACT: ACETATE ION(Non-functional Binders)
- 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
AB
BC
AD
B