SMTL ID : 8swu.1

Structure of Clostridium perfringens PNP bound to transition state analog IMMUCILLIN H and sulfate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-trimer

Ligands

3 x IMH: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL(Non-covalent)

IMH.1: 17 residues within 4Å: Chain A: H.84, Y.86, A.114, A.115, G.116, Y.193, E.194, V.210, G.211, M.212, T.235, N.236, L.246, H.248, V.251 Chain B: F.154 Ligands: SO4.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.86, A:Y.86, A:Y.193, A:Y.193, A:E.194, A:M.212, A:N.236, A:N.236 Water bridges: A:A.114 pi-Stacking: A:Y.193 IMH.3: 15 residues within 4Å: Chain B: A.114, A.115, G.116, Y.193, E.194, V.210, G.211, M.212, T.235, N.236, L.246, H.248, V.251 Chain C: F.154 Ligands: SO4.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.193, B:E.194, B:M.212, B:T.235, B:N.236, B:N.236, B:H.248 Water bridges: B:Y.185 pi-Stacking: B:Y.193 IMH.5: 16 residues within 4Å: Chain A: F.154 Chain C: H.84, A.114, A.115, G.116, Y.193, E.194, V.210, G.211, M.212, T.235, N.236, L.246, H.248, V.251 Ligands: SO4.6 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.193, C:Y.193, C:E.194, C:M.212, C:T.235, C:N.236, C:N.236 pi-Stacking: C:Y.193

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: G.30, R.82, H.84, N.113, A.114, S.213 Ligands: IMH.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.114, A:A.114, A:S.213 Water bridges: A:R.82, A:R.82, A:M.212 Salt bridges: A:R.82, A:H.84 SO4.4: 8 residues within 4Å: Chain B: G.30, S.31, R.82, H.84, N.113, A.114, S.213 Ligands: IMH.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.30, B:A.114, B:S.213 Water bridges: B:N.113, B:S.213 Salt bridges: B:R.82, B:H.84 SO4.6: 7 residues within 4Å: Chain C: G.30, R.82, H.84, N.113, A.114, S.213 Ligands: IMH.5 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.114, C:S.213, C:S.213 Salt bridges: C:R.82, C:H.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minnow, Y.V.T. et al., Phosphate Binding in PNP Alters Transition-State Analogue Affinity and Subunit Cooperativity. Biochemistry (2023)

Release Date

2023-10-18

Peptides

Purine nucleoside phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Purine nucleoside phosphorylase