SMTL ID : 1wta.2 (1 other biounit)

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine from Aeropyrum pernix (R32 form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: R.62, H.63, S.95, A.96, T.196 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.95, A:S.95, A:A.96, A:T.196 Water bridges: A:R.62, A:S.95, A:M.195, A:M.195 Salt bridges: A:R.62, A:H.63 PO4.3: 5 residues within 4Å: Chain B: R.62, H.63, S.95, A.96, T.196 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.95, B:S.95, B:A.96, B:T.196 Water bridges: B:R.62, B:S.95, B:M.195, B:M.195 Salt bridges: B:R.62, B:H.63 PO4.5: 5 residues within 4Å: Chain C: R.62, H.63, S.95, A.96, T.196 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.95, C:S.95, C:A.96, C:T.196 Water bridges: C:R.62, C:S.95, C:M.195, C:M.195 Salt bridges: C:R.62, C:H.63 PO4.7: 5 residues within 4Å: Chain D: R.62, H.63, S.95, A.96, T.196 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.95, D:S.95, D:A.96 Water bridges: D:R.62, D:M.195, D:M.195, D:T.196 Salt bridges: D:R.62, D:H.63 PO4.9: 5 residues within 4Å: Chain E: R.62, H.63, S.95, A.96, T.196 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:S.95, E:S.95, E:A.96 Water bridges: E:R.62, E:M.195, E:M.195, E:T.196 Salt bridges: E:R.62, E:H.63 PO4.11: 5 residues within 4Å: Chain F: R.62, H.63, S.95, A.96, T.196 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:S.95, F:S.95, F:A.96 Water bridges: F:R.62, F:M.195, F:M.195, F:T.196 Salt bridges: F:R.62, F:H.63

6 x ADE: ADENINE(Non-covalent)

ADE.2: 12 residues within 4Å: Chain A: A.96, V.97, G.98, F.175, I.193, G.194, M.195, T.218, D.219, D.221, V.228, V.233 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.98, A:D.221, A:D.221 Water bridges: A:M.195 pi-Stacking: A:F.175 ADE.4: 12 residues within 4Å: Chain B: A.96, V.97, G.98, F.175, I.193, G.194, M.195, T.218, D.219, D.221, V.228, V.233 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.98, B:D.221, B:D.221 Water bridges: B:M.195 pi-Stacking: B:F.175 ADE.6: 12 residues within 4Å: Chain C: A.96, V.97, G.98, F.175, I.193, G.194, M.195, T.218, D.219, D.221, V.228, V.233 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.98, C:D.221, C:D.221 Water bridges: C:M.195 pi-Stacking: C:F.175 ADE.8: 12 residues within 4Å: Chain D: A.96, V.97, G.98, F.175, I.193, G.194, M.195, T.218, D.219, D.221, V.228, V.233 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.98, D:T.218, D:D.221, D:D.221, D:D.221 Water bridges: D:M.195 pi-Stacking: D:F.175 ADE.10: 12 residues within 4Å: Chain E: A.96, V.97, G.98, F.175, I.193, G.194, M.195, T.218, D.219, D.221, V.228, V.233 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:G.98, E:T.218, E:D.221, E:D.221, E:D.221 Water bridges: E:M.195 pi-Stacking: E:F.175 ADE.12: 12 residues within 4Å: Chain F: A.96, V.97, G.98, F.175, I.193, G.194, M.195, T.218, D.219, D.221, V.228, V.233 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.98, F:T.218, F:D.221, F:D.221, F:D.221 Water bridges: F:M.195 pi-Stacking: F:F.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsunoda, M. et al., Crystal Structure of 5'-Deoxy-5'-methylthioadenosine from Aeropyrum pernix (R32 form). To be Published

Release Date

2006-02-07

Peptides

5'-methylthioadenosine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

5'-methylthioadenosine phosphorylase

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