SMTL ID : 5tc8.1

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with methylthio-DADMe-Immucillin-A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x TDI: (3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL(Non-covalent)

TDI.1: 17 residues within 4Å: Chain A: T.32, H.75, P.83, A.108, C.109, G.110, F.191, I.208, N.209, M.210, T.233, D.234, D.236, V.245, V.250 Chain C: H.151 Ligands: PO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.32, A:H.75, A:D.234, A:D.236, A:D.236 pi-Stacking: A:F.191 TDI.9: 17 residues within 4Å: Chain A: H.151 Chain B: T.32, H.75, P.83, A.108, C.109, G.110, F.191, I.208, N.209, M.210, T.233, D.234, D.236, V.245, V.250 Ligands: PO4.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.32, B:H.75, B:D.234, B:D.236, B:D.236 pi-Stacking: B:F.191 TDI.17: 17 residues within 4Å: Chain B: H.151 Chain C: T.32, H.75, P.83, A.108, C.109, G.110, F.191, I.208, N.209, M.210, T.233, D.234, D.236, V.245, V.250 Ligands: PO4.18 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.32, C:H.75, C:D.234, C:D.236, C:D.236 pi-Stacking: C:F.191

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

PO4.2: 8 residues within 4Å: Chain A: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: TDI.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.32, A:T.107, A:A.108 Water bridges: A:T.106 Salt bridges: A:R.74, A:H.75 PO4.10: 8 residues within 4Å: Chain B: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: TDI.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.32, B:T.107, B:A.108 Water bridges: B:T.106 Salt bridges: B:R.74, B:H.75 PO4.18: 8 residues within 4Å: Chain C: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: TDI.17 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.32, C:T.107, C:A.108 Water bridges: C:T.106 Salt bridges: C:R.74, C:H.75

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: MG.11, MG.19 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:T.132, B:T.132, A:T.132, H2O.7, H2O.21 MG.4: 1 residues within 4Å: Ligands: 2PE.6 No protein-ligand interaction detected (PLIP) MG.11: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: MG.3, MG.19 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:T.132, B:T.132, A:T.132, H2O.7, H2O.14 MG.12: 1 residues within 4Å: Ligands: 2PE.14 No protein-ligand interaction detected (PLIP) MG.19: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: MG.3, MG.11 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:T.132, A:T.132, B:T.132, H2O.14, H2O.21 MG.20: 1 residues within 4Å: Ligands: 2PE.22 No protein-ligand interaction detected (PLIP)

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.13, CL.21 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.5, CL.21 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligands: CL.5, CL.13 Ligand excluded by PLIP

3 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.6: 7 residues within 4Å: Chain A: K.171, G.174, L.175, R.176, C.177, H.178 Ligands: MG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.176 Water bridges: A:C.177, A:C.177 2PE.14: 7 residues within 4Å: Chain B: K.171, G.174, L.175, R.176, C.177, H.178 Ligands: MG.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.176 Water bridges: B:C.177, B:C.177 2PE.22: 7 residues within 4Å: Chain C: K.171, G.174, L.175, R.176, C.177, H.178 Ligands: MG.20 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.176 Water bridges: C:C.177, C:C.177

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 3 residues within 4Å: Chain A: S.84, K.85, M.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.85 Water bridges: A:K.85 PEG.8: 5 residues within 4Å: Chain A: W.93, K.96, E.97, Y.139, A.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.97, A:Y.139, A:E.221 PEG.15: 3 residues within 4Å: Chain B: S.84, K.85, M.133 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.85 Water bridges: B:K.85 PEG.16: 5 residues within 4Å: Chain B: W.93, K.96, E.97, Y.139, A.222 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.97, B:Y.139, B:E.221 PEG.23: 3 residues within 4Å: Chain C: S.84, K.85, M.133 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.85 Water bridges: C:K.85 PEG.24: 5 residues within 4Å: Chain C: W.93, K.96, E.97, Y.139, A.222 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.97, C:Y.139, C:E.221

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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