SMTL ID : 3t94.2 (1 other biounit)

Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) II complexed with 5'-deoxy-5'-methylthioadenosine and sulfate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-hexamer

Ligands

6 x MTA: 5'-DEOXY-5'-METHYLTHIOADENOSINE(Non-covalent)

MTA.1: 19 residues within 4Å: Chain A: S.16, H.59, P.67, A.92, V.93, G.94, I.165, F.170, I.188, G.189, M.190, T.213, D.214, D.216, A.225, V.228 Chain B: H.130, V.270 Ligands: SO4.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.16, A:H.59, A:M.190, A:T.213, A:D.214, A:D.216 pi-Stacking: A:F.170 MTA.4: 20 residues within 4Å: Chain B: S.16, H.59, P.67, A.92, V.93, G.94, I.165, F.170, I.188, G.189, M.190, T.213, D.214, D.216, A.225, V.228, T.229 Chain C: H.130, V.270 Ligands: SO4.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.16, B:H.59, B:M.190, B:T.213, B:D.216, B:D.216 pi-Stacking: B:F.170 MTA.7: 19 residues within 4Å: Chain A: H.130, V.270 Chain C: S.16, H.59, P.67, A.92, V.93, G.94, I.165, F.170, I.188, G.189, M.190, T.213, D.214, D.216, A.225, V.228 Ligands: SO4.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.16, C:H.59, C:M.190, C:T.213, C:D.216, C:D.216 Water bridges: C:Y.162 pi-Stacking: C:F.170 MTA.9: 19 residues within 4Å: Chain D: S.16, H.59, P.67, A.92, V.93, G.94, I.165, F.170, I.188, G.189, M.190, T.213, D.214, D.216, A.225, V.228 Chain E: H.130, V.270 Ligands: SO4.10 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.16, D:H.59, D:M.190, D:D.214 Water bridges: D:Y.162 pi-Stacking: D:F.170 MTA.12: 20 residues within 4Å: Chain E: S.16, H.59, P.67, A.92, V.93, G.94, I.165, F.170, I.188, G.189, M.190, T.213, D.214, D.216, A.225, V.228, T.229 Chain F: H.130, V.270 Ligands: SO4.13 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.16, E:H.59, E:M.190, E:D.216 Water bridges: E:Y.162 pi-Stacking: E:F.170 MTA.15: 19 residues within 4Å: Chain D: H.130, V.270 Chain F: S.16, H.59, P.67, A.92, V.93, G.94, I.165, F.170, I.188, G.189, M.190, T.213, D.214, D.216, A.225, V.228 Ligands: SO4.16 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.16, F:H.59, F:M.190, F:D.216 pi-Stacking: F:F.170

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

SO4.2: 8 residues within 4Å: Chain A: G.15, S.16, R.58, H.59, S.91, A.92, T.191 Ligands: MTA.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.16, A:A.92, A:T.191 Salt bridges: A:R.58, A:H.59 SO4.3: 5 residues within 4Å: Chain A: Q.38, P.39, R.64 Chain F: Q.38, R.64 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain A Salt bridges: F:R.64, A:R.64 Water bridges: A:Q.38, A:Q.38 SO4.5: 8 residues within 4Å: Chain B: G.15, S.16, R.58, H.59, S.91, A.92, T.191 Ligands: MTA.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.16, B:A.92, B:T.191, B:T.191 Salt bridges: B:R.58, B:H.59 SO4.6: 5 residues within 4Å: Chain B: Q.38, R.64 Chain E: Q.38, R.64 Ligands: SO4.14 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain E Water bridges: B:Q.38, B:Q.38, E:Q.38 Salt bridges: B:R.64, E:R.64 SO4.8: 8 residues within 4Å: Chain C: G.15, S.16, R.58, H.59, S.91, A.92, T.191 Ligands: MTA.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.16, C:A.92, C:T.191 Salt bridges: C:R.58, C:H.59 SO4.10: 8 residues within 4Å: Chain D: G.15, S.16, R.58, H.59, S.91, A.92, T.191 Ligands: MTA.9 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.16, D:A.92, D:T.191, D:T.191 Salt bridges: D:R.58, D:H.59 SO4.11: 5 residues within 4Å: Chain C: Q.38, R.64 Chain D: Q.38, P.39, R.64 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Salt bridges: C:R.64, D:R.64 Water bridges: D:Q.38, D:Q.38 SO4.13: 8 residues within 4Å: Chain E: G.15, S.16, R.58, H.59, S.91, A.92, T.191 Ligands: MTA.12 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.16, E:A.92, E:T.191 Salt bridges: E:R.58, E:H.59 SO4.14: 5 residues within 4Å: Chain B: Q.38, R.64 Chain E: Q.38, R.64 Ligands: SO4.6 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain E Water bridges: B:Q.38, E:Q.38, E:Q.38 Salt bridges: B:R.64, E:R.64 SO4.16: 8 residues within 4Å: Chain F: G.15, S.16, R.58, H.59, S.91, A.92, T.191 Ligands: MTA.15 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.16, F:A.92, F:T.191, F:T.191 Salt bridges: F:R.58, F:H.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., A corrected space group for Sulfolobus sulfataricus 5'-deoxy-5'-methylthioadenosine phosphorylase II. Acta Crystallogr.,Sect.D (2012)

Release Date

2011-08-24

Peptides

5'-methylthioadenosine phosphorylase (MtaP): ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
D

E
E

F
F

5'-methylthioadenosine phosphorylase (MtaP)

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