SMTL ID : 5tc7.1

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 5'-methylthiotubercidin at 1.75 angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: MTH.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.32, A:T.32, A:T.32, A:T.107, A:T.107, A:T.107, A:A.108, A:T.211 Salt bridges: A:R.74, A:H.75 PO4.2: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: PO4.7, PO4.12 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:M.133 Hydrogen bonds: A:T.132 PO4.3: 5 residues within 4Å: Chain A: R.113, E.114, E.115, R.201, W.238 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.114, A:E.115 Salt bridges: A:R.113, A:R.201 PO4.6: 8 residues within 4Å: Chain B: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: MTH.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.32, B:T.32, B:T.32, B:T.107, B:T.107, B:T.107, B:A.108, B:T.211 Salt bridges: B:R.74, B:H.75 PO4.7: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: PO4.2, PO4.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:M.133 Hydrogen bonds: B:T.132 PO4.8: 5 residues within 4Å: Chain B: R.113, E.114, E.115, R.201, W.238 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.114, B:E.115 Salt bridges: B:R.113, B:R.201 PO4.11: 8 residues within 4Å: Chain C: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: MTH.14 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.32, C:T.32, C:T.32, C:T.107, C:T.107, C:T.107, C:A.108, C:T.211 Salt bridges: C:R.74, C:H.75 PO4.12: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: PO4.2, PO4.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:M.133 Hydrogen bonds: C:T.132 PO4.13: 5 residues within 4Å: Chain C: R.113, E.114, E.115, R.201, W.238 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.114, C:E.115 Salt bridges: C:R.113, C:R.201

3 x MTH: 2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-METHYLSULFANYLMETHYL-TETRAHYDRO-FURAN-3,4-DIOL(Non-covalent)

MTH.4: 20 residues within 4Å: Chain A: T.32, H.75, P.83, A.108, C.109, G.110, I.186, F.191, I.208, N.209, M.210, T.211, T.233, D.234, D.236, V.245, V.250 Chain B: H.151, L.293 Ligands: PO4.1 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.250 Hydrogen bonds: A:M.210, A:D.236 Water bridges: A:H.75, B:H.151 pi-Stacking: A:F.191 MTH.9: 20 residues within 4Å: Chain B: T.32, H.75, P.83, A.108, C.109, G.110, I.186, F.191, I.208, N.209, M.210, T.211, T.233, D.234, D.236, V.245, V.250 Chain C: H.151, L.293 Ligands: PO4.6 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.250 Hydrogen bonds: B:M.210, B:D.236 Water bridges: B:H.75, C:H.151 pi-Stacking: B:F.191 MTH.14: 20 residues within 4Å: Chain A: H.151, L.293 Chain C: T.32, H.75, P.83, A.108, C.109, G.110, I.186, F.191, I.208, N.209, M.210, T.211, T.233, D.234, D.236, V.245, V.250 Ligands: PO4.11 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C Water bridges: A:H.151, C:H.75 Hydrophobic interactions: C:V.250 Hydrogen bonds: C:M.210, C:D.236 pi-Stacking: C:F.191

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.10, CL.15 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.5, CL.15 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.5, CL.10 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Firestone, R.S. et al., TBA. To be published

Release Date

2017-10-11

Peptides

S-methyl-5'-thioadenosine phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

S-methyl-5'-thioadenosine phosphorylase

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