SMTL ID : 3k8q.1

Crystal structure of human purine nucleoside phosphorylase in complex with SerMe-Immucillin H

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x 22A: 7-({[2-hydroxy-1-(hydroxymethyl)ethyl]amino}methyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one(Non-covalent)

22A.1: 16 residues within 4Å: Chain A: Y.88, A.116, A.117, G.118, F.200, E.201, V.217, G.218, M.219, T.242, N.243, V.245, H.257, V.260 Chain C: F.159 Ligands: PO4.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.86, A:Y.88, A:E.201, A:N.243, A:N.243, A:H.257 Water bridges: A:H.86, A:M.219 pi-Stacking: A:F.200 22A.4: 16 residues within 4Å: Chain A: F.159 Chain B: Y.88, A.116, A.117, G.118, F.200, E.201, V.217, G.218, M.219, T.242, N.243, V.245, H.257, V.260 Ligands: PO4.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.86, B:Y.88, B:E.201, B:N.243, B:N.243, B:H.257 Water bridges: B:H.86, B:M.219 pi-Stacking: B:F.200 22A.7: 16 residues within 4Å: Chain B: F.159 Chain C: Y.88, A.116, A.117, G.118, F.200, E.201, V.217, G.218, M.219, T.242, N.243, V.245, H.257, V.260 Ligands: PO4.8 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:H.86, C:Y.88, C:E.201, C:N.243, C:N.243, C:H.257 Water bridges: C:H.86, C:M.219 pi-Stacking: C:F.200

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

PO4.2: 8 residues within 4Å: Chain A: G.32, S.33, R.84, H.86, N.115, A.116, S.220 Ligands: 22A.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.33, A:A.116, A:S.220, A:S.220 Water bridges: A:N.115, A:M.219, A:M.219 Salt bridges: A:R.84, A:H.86 PO4.3: 3 residues within 4Å: Chain A: R.148 Chain B: P.92, Q.144 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.148 Hydrogen bonds: B:Q.144 Water bridges: B:W.94 PO4.5: 8 residues within 4Å: Chain B: G.32, S.33, R.84, H.86, N.115, A.116, S.220 Ligands: 22A.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.33, B:A.116, B:S.220, B:S.220 Water bridges: B:N.115, B:M.219, B:M.219 Salt bridges: B:R.84, B:H.86 PO4.6: 3 residues within 4Å: Chain B: R.148 Chain C: P.92, Q.144 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.144 Water bridges: C:W.94 Salt bridges: B:R.148 PO4.8: 8 residues within 4Å: Chain C: G.32, S.33, R.84, H.86, N.115, A.116, S.220 Ligands: 22A.7 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.33, C:A.116, C:S.220, C:S.220 Water bridges: C:N.115, C:M.219, C:M.219 Salt bridges: C:R.84, C:H.86 PO4.9: 3 residues within 4Å: Chain A: P.92, Q.144 Chain C: R.148 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.144 Water bridges: A:W.94 Salt bridges: C:R.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ho, M. et al., Crystal structure of human nucleoside phosphorylase in complex with SerMe-ImmH. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-03-02

Peptides

Purine nucleoside phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Purine nucleoside phosphorylase

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