SMTL ID : 1zco.1

Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: P.61, G.113, A.114, R.115 Ligands: PEP.2 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain B: G.113, A.114, R.115 Ligands: PEP.5 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain C: P.61, G.113, A.114, R.115 Ligands: PEP.7 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain D: G.113, A.114, R.115 Ligands: PEP.10 Ligand excluded by PLIP

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 11 residues within 4Å: Chain A: R.55, E.93, Q.111, G.113, A.114, R.115, K.136, R.166, D.198, H.201 Ligands: CL.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.111, A:A.114, A:R.115, A:D.198 Salt bridges: A:R.55, A:K.136, A:K.136, A:R.166, A:H.201, A:H.201 PEP.5: 13 residues within 4Å: Chain B: R.55, K.60, P.61, E.93, Q.111, G.113, A.114, R.115, K.136, R.166, D.198, H.201 Ligands: CL.4 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:P.61 Hydrogen bonds: B:E.93, B:Q.111, B:A.114, B:R.115, B:D.198, B:D.198 Salt bridges: B:R.55, B:K.60, B:K.136, B:K.136, B:R.166, B:H.201, B:H.201 PEP.7: 11 residues within 4Å: Chain C: R.55, E.93, Q.111, G.113, A.114, R.115, K.136, R.166, D.198, H.201 Ligands: CL.6 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.111, C:A.114, C:R.115 Salt bridges: C:R.55, C:K.136, C:K.136, C:R.166, C:H.201, C:H.201 PEP.10: 13 residues within 4Å: Chain D: R.55, K.60, P.61, E.93, Q.111, G.113, A.114, R.115, K.136, R.166, D.198, H.201 Ligands: CL.9 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:P.61 Hydrogen bonds: D:Q.111, D:A.114, D:R.115, D:D.198, D:D.198, D:D.198 Salt bridges: D:R.55, D:K.60, D:K.136, D:K.136, D:R.166, D:H.201, D:H.201

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 4 residues within 4Å: Chain B: C.31, H.201, E.227, D.238 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.31, B:H.201, B:E.227, B:D.238 MN.8: 4 residues within 4Å: Chain D: C.31, H.201, E.227, D.238 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.31, D:H.201, D:E.227, D:D.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schofield, L.R. et al., Substrate Ambiguity and Crystal Structure of Pyrococcus furiosus 3-Deoxy-d-arabino-heptulosonate-7-phosphate Synthase: An Ancestral 3-Deoxyald-2-ulosonate-phosphate Synthase?(,). Biochemistry (2005)

Release Date

2005-10-18

Peptides

2-dehydro-3-deoxyphosphoheptonate aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

2-dehydro-3-deoxyphosphoheptonate aldolase