SMTL ID : 2r87.1 (1 other biounit)

Crystal structure of PurP from Pyrococcus furiosus complexed with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

10 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: H.11, R.202, R.287, V.289, A.290 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.290 Water bridges: A:K.137, A:G.291 Salt bridges: A:H.11, A:R.202, A:R.287 PO4.2: 4 residues within 4Å: Chain A: R.191, Y.306, R.308, M.318 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.191, A:R.308 PO4.3: 6 residues within 4Å: Chain A: R.238, S.240 Chain B: S.10, H.11, S.71, H.75 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.10, B:S.10, B:H.11, B:S.71, A:S.240, A:S.240 Water bridges: A:S.240 Salt bridges: A:R.238 PO4.5: 5 residues within 4Å: Chain B: H.11, R.202, R.287, V.289, A.290 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.290 Water bridges: B:G.291 Salt bridges: B:H.11, B:R.202, B:R.287 PO4.6: 4 residues within 4Å: Chain B: R.191, Y.306, R.308, M.318 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.191, B:R.308 PO4.7: 4 residues within 4Å: Chain B: R.238, S.240 Chain C: S.10, S.71 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.240, C:S.10, C:S.10, C:S.71 Water bridges: B:S.240, C:H.11 Salt bridges: B:R.238 PO4.9: 4 residues within 4Å: Chain A: S.10, S.71 Chain C: R.238, S.240 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:S.240, A:S.10, A:S.10, A:S.10, A:S.71 Water bridges: C:S.240, C:S.240 Salt bridges: C:R.238 PO4.10: 5 residues within 4Å: Chain C: H.11, R.202, R.287, V.289, A.290 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.290 Salt bridges: C:H.11, C:R.202, C:R.287 PO4.11: 3 residues within 4Å: Chain C: R.105, K.109, V.118 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.105 Salt bridges: C:R.105, C:K.109 PO4.12: 4 residues within 4Å: Chain C: R.191, Y.306, R.308, M.318 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.191, C:R.308

3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 18 residues within 4Å: Chain A: P.116, I.130, K.132, G.138, G.139, Y.142, Q.173, E.174, Y.175, V.176, Y.182, R.202, E.204, Y.227, E.270, F.282, E.283 Chain B: R.212 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.132, A:G.138, A:G.139, A:Q.173, A:V.176, A:Y.182, A:E.204, B:R.212 Water bridges: A:K.137, A:Y.182, A:R.202, B:R.212 Salt bridges: A:K.132, A:R.202, A:R.202 pi-Stacking: A:F.282, A:F.282 ADP.8: 19 residues within 4Å: Chain B: P.116, I.130, K.132, K.137, G.138, G.139, Y.142, Q.173, E.174, Y.175, V.176, Y.182, R.202, E.204, Y.227, E.270, F.282, E.283 Chain C: R.212 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.132, B:A.136, B:G.138, B:G.139, B:Q.173, B:V.176, B:Y.182, B:R.202, B:E.204, C:R.212 Water bridges: B:Y.182 Salt bridges: B:K.132 pi-Stacking: B:F.282, B:F.282 ADP.13: 19 residues within 4Å: Chain A: R.212 Chain C: P.116, I.130, K.132, K.137, G.138, G.139, Y.142, Q.173, E.174, Y.175, V.176, Y.182, R.202, E.204, Y.227, E.270, F.282, E.283 17 PLIP interactions: 1 interactions with chain A, 16 interactions with chain C Hydrogen bonds: A:R.212, C:K.132, C:G.138, C:G.139, C:Y.142, C:Q.173, C:V.176, C:Y.182, C:R.202, C:E.204 Water bridges: C:K.137, C:K.137, C:Y.182 Salt bridges: C:K.132, C:K.137 pi-Stacking: C:F.282, C:F.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii. Biochemistry (2008)

Release Date

2007-12-04

Peptides

PurP protein PF1517: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

PurP protein PF1517

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