SMTL ID : 3ut6.1

Crystal structure of E. Coli PNP complexed with PO4 and formycin A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-hexamer

Ligands

6 x FMC: (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol(Non-covalent)

FMC.1: 16 residues within 4Å: Chain A: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204, I.206 Chain C: H.4, R.43 Ligands: PO4.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.87, A:S.90, A:M.180, A:E.181, A:S.203, A:D.204, A:D.204, C:H.4, C:R.43 Water bridges: A:R.217, A:R.217 FMC.3: 15 residues within 4Å: Chain B: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204, I.206 Chain E: H.4, R.43 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:R.87, B:S.90, B:G.92, B:M.180, B:E.181, B:S.203, B:D.204, B:D.204, E:H.4, E:R.43 Water bridges: B:R.87, B:S.90, E:R.43, E:R.43 FMC.6: 15 residues within 4Å: Chain A: H.4, R.43 Chain C: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204, I.206 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:R.87, C:R.87, C:S.90, C:M.180, C:E.181, C:S.203, C:D.204, C:D.204, A:H.4, A:R.43 Water bridges: C:S.90, A:R.43, A:R.43 FMC.9: 16 residues within 4Å: Chain D: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204, I.206 Chain F: H.4, R.43 Ligands: PO4.10 12 PLIP interactions: 2 interactions with chain F, 10 interactions with chain D Hydrogen bonds: F:H.4, F:R.43, D:R.87, D:S.90, D:M.180, D:E.181, D:S.203, D:D.204, D:D.204 Water bridges: D:D.204, D:R.217, D:R.217 FMC.11: 15 residues within 4Å: Chain B: H.4, R.43 Chain E: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204, I.206 14 PLIP interactions: 10 interactions with chain E, 4 interactions with chain B Hydrogen bonds: E:R.87, E:S.90, E:G.92, E:M.180, E:E.181, E:S.203, E:D.204, E:D.204, B:H.4, B:R.43 Water bridges: E:R.87, E:S.90, B:R.43, B:R.43 FMC.14: 15 residues within 4Å: Chain D: H.4, R.43 Chain F: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, D.204, I.206 13 PLIP interactions: 9 interactions with chain F, 4 interactions with chain D Hydrogen bonds: F:R.87, F:R.87, F:S.90, F:M.180, F:E.181, F:S.203, F:D.204, F:D.204, D:H.4, D:R.43 Water bridges: F:S.90, D:R.43, D:R.43

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

PO4.2: 10 residues within 4Å: Chain A: P.19, G.20, D.21, R.24, R.87, G.89, S.90, E.181 Chain C: R.43 Ligands: FMC.1 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.20, A:D.21, A:V.88, A:S.90, A:S.90 Water bridges: A:S.90 Salt bridges: A:R.24, A:R.87, C:R.43 PO4.4: 10 residues within 4Å: Chain B: P.19, G.20, D.21, R.24, V.88, G.89, S.90, F.221, M.224 Ligands: PO4.5 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:G.20, B:D.21, B:R.87 Water bridges: B:S.90, B:S.90, B:S.90, E:R.43, E:R.43, E:R.43 PO4.5: 5 residues within 4Å: Chain B: D.21, R.24, S.90, R.217 Ligands: PO4.4 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:S.90 Salt bridges: B:R.24, B:R.217, E:R.43 Water bridges: E:R.43 PO4.7: 4 residues within 4Å: Chain A: R.43 Chain C: D.21, R.24 Ligands: PO4.8 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Water bridges: A:R.43, C:R.24, C:S.90 Salt bridges: A:R.43, C:R.24 Hydrogen bonds: C:D.21 PO4.8: 9 residues within 4Å: Chain C: P.19, G.20, D.21, R.24, V.88, G.89, S.90, F.221 Ligands: PO4.7 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain C Water bridges: A:R.43, A:R.43, A:R.43, A:R.43 Hydrogen bonds: C:G.20, C:D.21, C:R.87, C:V.88, C:S.90, C:S.90 PO4.10: 10 residues within 4Å: Chain D: P.19, G.20, D.21, R.24, R.87, G.89, S.90, E.181 Chain F: R.43 Ligands: FMC.9 9 PLIP interactions: 1 interactions with chain F, 8 interactions with chain D Salt bridges: F:R.43, D:R.24, D:R.87 Hydrogen bonds: D:G.20, D:D.21, D:V.88, D:S.90, D:S.90 Water bridges: D:S.90 PO4.12: 10 residues within 4Å: Chain E: P.19, G.20, D.21, R.24, V.88, G.89, S.90, F.221, M.224 Ligands: PO4.13 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:G.20, E:D.21, E:R.87 Water bridges: E:S.90, E:S.90, E:S.90, B:R.43, B:R.43, B:R.43 PO4.13: 5 residues within 4Å: Chain E: D.21, R.24, S.90, R.217 Ligands: PO4.12 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:D.21, E:S.90 Salt bridges: E:R.24, E:R.217, B:R.43 Water bridges: B:R.43 PO4.15: 4 residues within 4Å: Chain D: R.43 Chain F: D.21, R.24 Ligands: PO4.16 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain D Water bridges: F:R.24, F:S.90, D:R.43 Salt bridges: F:R.24, D:R.43 PO4.16: 9 residues within 4Å: Chain F: P.19, G.20, D.21, R.24, V.88, G.89, S.90, F.221 Ligands: PO4.15 10 PLIP interactions: 6 interactions with chain F, 4 interactions with chain D Hydrogen bonds: F:G.20, F:D.21, F:R.87, F:V.88, F:S.90, F:S.90 Water bridges: D:R.43, D:R.43, D:R.43, D:R.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stefanic, Z. et al., New phosphate binding sites in the crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with phosphate and formycin A. Febs Lett. (2012)

Release Date

2012-05-23

Peptides

Purine nucleoside phosphorylase deoD-type: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Purine nucleoside phosphorylase deoD-type

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