SMTL ID : 2i14.1

Crystal structure of nicotinate-nucleotide pyrophosphorylase from Pyrococcus furiosus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.333, N.335, H.337, C.350, V.352, C.353 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.333, A:H.337, A:C.350, A:C.353 ZN.2: 3 residues within 4Å: Chain A: H.184, D.215, D.241 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.184, A:D.241, A:D.241 ZN.4: 6 residues within 4Å: Chain B: C.333, N.335, H.337, C.350, V.352, C.353 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.333, B:H.337, B:C.350, B:C.353 ZN.5: 3 residues within 4Å: Chain B: H.184, D.215, D.241 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.184, B:D.241, B:D.241 ZN.7: 6 residues within 4Å: Chain C: C.333, N.335, H.337, C.350, V.352, C.353 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.333, C:H.337, C:C.350, C:C.353 ZN.8: 3 residues within 4Å: Chain C: H.184, D.215, D.241 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.184, C:D.241, C:D.241 ZN.10: 6 residues within 4Å: Chain D: C.333, N.335, H.337, C.350, V.352, C.353 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.333, D:H.337, D:C.350, D:C.353 ZN.11: 3 residues within 4Å: Chain D: H.184, D.215, D.241 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.184, D:D.215, D:D.241, D:D.241 ZN.13: 6 residues within 4Å: Chain E: C.333, N.335, H.337, C.350, V.352, C.353 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.333, E:H.337, E:C.350, E:C.353 ZN.14: 3 residues within 4Å: Chain E: H.184, D.215, D.241 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.184, E:D.241, E:D.241 ZN.16: 6 residues within 4Å: Chain F: C.333, N.335, H.337, C.350, V.352, C.353 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.333, F:H.337, F:C.350, F:C.353 ZN.17: 3 residues within 4Å: Chain F: H.184, D.215, D.241 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.184, F:D.241, F:D.241

6 x PCP: 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE(Non-covalent)

PCP.3: 13 residues within 4Å: Chain A: F.140, R.143, H.144, P.183, H.184, R.239, D.241, S.274, G.275, G.276, G.295, G.296 Chain B: Y.27 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.140 Hydrogen bonds: A:R.143, A:H.184, A:D.241, A:G.276, A:L.277, A:G.295, A:G.296, B:Y.27 Salt bridges: A:H.144, A:H.184, A:R.239, A:R.239 PCP.6: 13 residues within 4Å: Chain A: Y.27 Chain B: F.140, R.143, H.144, P.183, H.184, R.239, D.241, S.274, G.275, G.276, G.295, G.296 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.140 Hydrogen bonds: B:R.143, B:H.184, B:G.276, B:L.277, B:G.295, B:G.296, A:Y.27 Water bridges: B:R.143 Salt bridges: B:H.144, B:H.184, B:R.239, B:R.239 PCP.9: 13 residues within 4Å: Chain C: F.140, R.143, H.144, P.183, H.184, R.239, D.241, S.274, G.275, G.276, G.295, G.296 Chain D: Y.27 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.140 Hydrogen bonds: C:R.143, C:H.184, C:G.276, C:L.277, C:G.295, C:G.296, D:Y.27 Salt bridges: C:H.144, C:H.184, C:R.239, C:R.239 PCP.12: 13 residues within 4Å: Chain C: Y.27 Chain D: F.140, R.143, H.144, P.183, H.184, R.239, D.241, S.274, G.275, G.276, G.295, G.296 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.140 Hydrogen bonds: D:R.143, D:H.184, D:G.276, D:L.277, D:G.295, D:G.296, C:Y.27 Salt bridges: D:H.144, D:H.184, D:R.239, D:R.239 Water bridges: C:Y.27 PCP.15: 13 residues within 4Å: Chain E: F.140, R.143, H.144, P.183, H.184, R.239, D.241, S.274, G.275, G.276, G.295, G.296 Chain F: Y.27 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:F.140 Hydrogen bonds: E:R.143, E:H.184, E:G.276, E:L.277, E:G.295, E:G.296, F:Y.27 Water bridges: E:F.140, E:R.239, F:Y.27 Salt bridges: E:H.144, E:H.184, E:R.239, E:R.239 PCP.18: 13 residues within 4Å: Chain E: Y.27 Chain F: F.140, R.143, H.144, P.183, H.184, R.239, D.241, S.274, G.275, G.276, G.295, G.296 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:F.140 Hydrogen bonds: F:R.143, F:H.184, F:G.276, F:L.277, F:G.295, F:G.296, E:Y.27 Water bridges: F:R.239 Salt bridges: F:H.144, F:H.184, F:R.239, F:R.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, D.H. et al., Crystal structure of nicotinate-nucleotide pyrophosphorylase from Pyrococcus furiosus. To be Published

Release Date

2006-10-10

Peptides

Nicotinate-nucleotide pyrophosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nicotinate-nucleotide pyrophosphorylase