SMTL ID : 5eub.1

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 2-amino-MTA and sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: 5S7.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.32, A:T.32, A:T.32, A:T.107, A:A.108, A:T.211, A:T.211 Water bridges: A:T.211 Salt bridges: A:R.74, A:H.75 SO4.2: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: SO4.8, SO4.14 No protein-ligand interaction detected (PLIP) SO4.7: 8 residues within 4Å: Chain B: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: 5S7.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.32, B:T.32, B:T.32, B:T.107, B:A.108, B:T.211, B:T.211 Water bridges: B:T.211 Salt bridges: B:R.74, B:H.75 SO4.8: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: SO4.2, SO4.14 No protein-ligand interaction detected (PLIP) SO4.13: 8 residues within 4Å: Chain C: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: 5S7.15 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.32, C:T.32, C:T.32, C:T.107, C:A.108, C:T.211, C:T.211 Water bridges: C:T.211 Salt bridges: C:R.74, C:H.75 SO4.14: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: SO4.2, SO4.8 No protein-ligand interaction detected (PLIP)

3 x 5S7: (2~{R},3~{R},4~{S},5~{S})-2-[2,6-bis(azanyl)purin-9-yl]-5-(methylsulfanylmethyl)oxolane-3,4-diol(Non-covalent)

5S7.3: 18 residues within 4Å: Chain A: T.32, A.108, C.109, G.110, I.186, F.191, I.208, N.209, M.210, T.233, D.234, D.236, V.245, V.247, V.250, L.251 Chain B: H.151 Ligands: SO4.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.32, A:M.210, A:D.234 Water bridges: A:A.108, A:S.192, A:S.192 Salt bridges: A:D.236 pi-Stacking: A:F.191 5S7.9: 18 residues within 4Å: Chain B: T.32, A.108, C.109, G.110, I.186, F.191, I.208, N.209, M.210, T.233, D.234, D.236, V.245, V.247, V.250, L.251 Chain C: H.151 Ligands: SO4.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.32, B:M.210, B:D.234 Water bridges: B:A.108, B:S.192, B:S.192 Salt bridges: B:D.236 pi-Stacking: B:F.191 5S7.15: 18 residues within 4Å: Chain A: H.151 Chain C: T.32, A.108, C.109, G.110, I.186, F.191, I.208, N.209, M.210, T.233, D.234, D.236, V.245, V.247, V.250, L.251 Ligands: SO4.13 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.32, C:M.210, C:D.234 Water bridges: C:A.108, C:S.192, C:S.192 Salt bridges: C:D.236 pi-Stacking: C:F.191

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

CL.4: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.10, CL.16 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.4, CL.16 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.4, CL.10 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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:R.113, A:E.114, A:R.201, A:R.201 GOL.6: 5 residues within 4Å: Chain A: I.64, K.65, L.266, T.267, P.270 No protein-ligand interaction detected (PLIP) GOL.11: 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:R.113, B:E.114, B:R.201, B:R.201 GOL.12: 5 residues within 4Å: Chain B: I.64, K.65, L.266, T.267, P.270 No protein-ligand interaction detected (PLIP) GOL.17: 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:R.113, C:E.114, C:R.201, C:R.201 GOL.18: 5 residues within 4Å: Chain C: I.64, K.65, L.266, T.267, P.270 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Firestone, R.S. et al., Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 2-amino-MTA and sulfate. To be published

Release Date

2016-12-21

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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