SMTL ID : 3of3.1 (1 other biounit)

Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-hexamer

Ligands

6 x DIH: 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one(Non-covalent)

DIH.1: 15 residues within 4Å: Chain A: M.65, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, S.204, D.205, I.207 Chain C: H.5, R.44 Ligands: PO4.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.205, C:H.5 Water bridges: A:R.218 Salt bridges: A:E.182 DIH.3: 15 residues within 4Å: Chain B: M.65, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, S.204, D.205, I.207 Chain E: H.5, R.44 Ligands: PO4.4 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:D.205, E:H.5 Salt bridges: B:E.182 Water bridges: E:R.44 DIH.5: 15 residues within 4Å: Chain A: H.5, R.44 Chain C: M.65, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, S.204, D.205, I.207 Ligands: PO4.6 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:H.5, A:R.44, C:D.205 Salt bridges: C:E.182 DIH.7: 15 residues within 4Å: Chain D: M.65, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, S.204, D.205, I.207 Chain F: H.5, R.44 Ligands: PO4.8 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:H.5, D:D.205 Salt bridges: D:E.182 DIH.9: 14 residues within 4Å: Chain B: H.5, R.44 Chain E: M.65, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, S.204, D.205 Ligands: PO4.10 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:H.5, E:D.205, E:D.205 Salt bridges: E:E.182 DIH.11: 15 residues within 4Å: Chain D: H.5, R.44 Chain F: M.65, S.91, C.92, G.93, F.160, V.179, E.180, M.181, E.182, S.204, D.205, I.207 Ligands: PO4.12 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:D.205, F:D.205, D:H.5 Water bridges: F:R.218 Salt bridges: F:E.182

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

PO4.2: 9 residues within 4Å: Chain A: P.20, G.21, R.25, R.88, G.90, S.91, E.182 Chain C: R.44 Ligands: DIH.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.21, A:S.91 Salt bridges: A:R.25, A:R.88, C:R.44 PO4.4: 8 residues within 4Å: Chain B: P.20, G.21, R.25, R.88, G.90, S.91 Chain E: R.44 Ligands: DIH.3 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:G.21, B:V.89, B:S.91, B:S.91 Water bridges: B:S.204 Salt bridges: B:R.25, B:R.88, E:R.44 PO4.6: 9 residues within 4Å: Chain A: R.44 Chain C: P.20, G.21, R.25, R.88, G.90, S.91, E.182 Ligands: DIH.5 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.21, C:S.91, C:S.91, C:S.91 Water bridges: C:S.91 Salt bridges: C:R.25, C:R.88, A:R.44 PO4.8: 8 residues within 4Å: Chain D: P.20, G.21, R.25, R.88, G.90, S.91 Chain F: R.44 Ligands: DIH.7 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:G.21, D:S.91, D:S.91 Salt bridges: D:R.25, D:R.88, F:R.44 Water bridges: F:R.44 PO4.10: 8 residues within 4Å: Chain B: R.44 Chain E: P.20, G.21, R.25, R.88, G.90, S.91 Ligands: DIH.9 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:G.21, E:S.91 Salt bridges: E:R.25, E:R.88, B:R.44 PO4.12: 9 residues within 4Å: Chain D: R.44 Chain F: P.20, G.21, R.25, R.88, G.90, S.91, E.182 Ligands: DIH.11 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:G.21, F:S.91, F:S.91 Water bridges: F:S.91 Salt bridges: F:R.25, F:R.88, D:R.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J. et al., Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae. To be Published

Release Date

2010-09-01

Peptides

Purine nucleoside phosphorylase deoD-type 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
L

Purine nucleoside phosphorylase deoD-type 1

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