SMTL ID : 2r86.1 (1 other biounit)

Crystal structure of PurP from Pyrococcus furiosus complexed with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: S.10, S.71, H.75 Chain B: R.238, S.240 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.10, A:S.10, A:S.71, B:S.240 Water bridges: A:H.11, B:R.238, B:S.240 Salt bridges: A:H.75, B:R.238 PO4.2: 5 residues within 4Å: Chain A: H.11, R.202, R.287, V.289, A.290 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.290 Water bridges: A:R.202, A:N.232, A:E.270, A:G.291 Salt bridges: A:H.11, A:R.202, A:R.287 PO4.7: 5 residues within 4Å: Chain B: S.10, S.71, H.75 Chain C: R.238, S.240 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.10, B:S.10, B:S.71, C:S.240 Water bridges: B:H.11, C:R.238, C:S.240 Salt bridges: B:H.75, C:R.238 PO4.8: 5 residues within 4Å: Chain B: H.11, R.202, R.287, V.289, A.290 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:A.290 Water bridges: B:R.202, B:N.232, B:E.270, B:G.291 Salt bridges: B:H.11, B:R.202, B:R.287 PO4.13: 5 residues within 4Å: Chain A: R.238, S.240 Chain C: S.10, S.71, H.75 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:S.10, C:S.10, C:S.71, A:S.240 Water bridges: C:H.11, A:R.238, A:S.240 Salt bridges: C:H.75, A:R.238 PO4.14: 5 residues within 4Å: Chain C: H.11, R.202, R.287, V.289, A.290 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:A.290 Water bridges: C:R.202, C:N.232, C:E.270, C:G.291 Salt bridges: C:H.11, C:R.202, C:R.287

3 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: E.98, E.104, E.283, I.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.283, A:E.283 NA.9: 4 residues within 4Å: Chain B: E.98, E.104, E.283, I.284 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.283, B:E.283 NA.15: 4 residues within 4Å: Chain C: E.98, E.104, E.283, I.284 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.283, C:E.283

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 15 residues within 4Å: Chain A: P.116, I.130, K.132, A.136, G.138, Y.142, Q.173, E.174, Y.175, V.176, Y.227, F.282, E.283 Chain C: R.212 Ligands: MPD.5 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.132, A:A.136, A:G.138, A:Q.173, A:V.176, C:R.212 Water bridges: A:R.202, A:R.202 Salt bridges: A:K.132 pi-Stacking: A:F.282, A:F.282 ATP.10: 15 residues within 4Å: Chain A: R.212 Chain B: P.116, I.130, K.132, A.136, G.138, Y.142, Q.173, E.174, Y.175, V.176, Y.227, F.282, E.283 Ligands: MPD.11 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:R.212, B:K.132, B:A.136, B:G.138, B:Q.173, B:V.176 Water bridges: B:R.202, B:R.202 Salt bridges: B:K.132 pi-Stacking: B:F.282, B:F.282 ATP.16: 15 residues within 4Å: Chain B: R.212 Chain C: P.116, I.130, K.132, A.136, G.138, Y.142, Q.173, E.174, Y.175, V.176, Y.227, F.282, E.283 Ligands: MPD.17 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.132, C:A.136, C:G.138, C:Q.173, C:V.176, B:R.212 Water bridges: C:R.202, C:R.202 Salt bridges: C:K.132 pi-Stacking: C:F.282, C:F.282

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 7 residues within 4Å: Chain A: I.130, Y.142, L.144, Y.227 Chain C: P.214, D.217 Ligands: ATP.4 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.142, A:L.144, A:Y.227, C:P.214 Hydrogen bonds: C:D.217, C:D.217 MPD.6: 7 residues within 4Å: Chain A: L.144, Y.175, L.177 Chain C: I.213, D.217, F.221, M.223 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.221, C:F.221, C:M.223, A:L.144, A:L.177 Hydrogen bonds: A:Y.175 MPD.11: 7 residues within 4Å: Chain A: P.214, D.217 Chain B: I.130, Y.142, L.144, Y.227 Ligands: ATP.10 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.214, B:Y.142, B:L.144, B:Y.227 Hydrogen bonds: A:D.217, A:D.217 MPD.12: 7 residues within 4Å: Chain A: I.213, D.217, F.221, M.223 Chain B: L.144, Y.175, L.177 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.221, A:F.221, A:M.223, B:L.144, B:L.177 Hydrogen bonds: B:Y.175 MPD.17: 7 residues within 4Å: Chain B: P.214, D.217 Chain C: I.130, Y.142, L.144, Y.227 Ligands: ATP.16 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Y.142, C:L.144, C:Y.227, B:P.214 Hydrogen bonds: B:D.217, B:D.217 MPD.18: 7 residues within 4Å: Chain B: I.213, D.217, F.221, M.223 Chain C: L.144, Y.175, L.177 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.144, C:L.177, B:F.221, B:F.221, B:M.223 Hydrogen bonds: C:Y.175

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
A

C
A

PurP protein PF1517

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