SMTL ID : 5tc6.1

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with propylthio-immucillin-A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-trimer

Ligands

3 x 7A6: (2S,3S,4R,5S)-2-(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-[(propylsulfanyl)methyl]pyrrolidine-3,4-diol(Non-covalent)

7A6.1: 21 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.247, V.250, L.251 Chain C: H.151 Ligands: PO4.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:T.32, A:V.247, A:L.251 Hydrogen bonds: A:T.32, A:M.210, A:T.233, A:D.234, A:D.236, A:D.236 Water bridges: A:H.75, C:H.151 pi-Stacking: A:F.191 7A6.6: 21 residues within 4Å: Chain A: H.151 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.247, V.250, L.251 Ligands: PO4.7 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.32, B:V.247, B:L.251 Hydrogen bonds: B:T.32, B:M.210, B:T.233, B:D.234, B:D.236, B:D.236 Water bridges: B:H.75, A:H.151 pi-Stacking: B:F.191 7A6.11: 21 residues within 4Å: Chain B: H.151 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.247, V.250, L.251 Ligands: PO4.12 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.32, C:V.247, C:L.251 Hydrogen bonds: C:T.32, C:M.210, C:T.233, C:D.234, C:D.236, C:D.236 Water bridges: C:H.75, B:H.151 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: 7A6.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.32, A:T.107, A:A.108 Salt bridges: A:R.74, A:H.75 PO4.7: 8 residues within 4Å: Chain B: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: 7A6.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.32, B:T.107, B:A.108 Salt bridges: B:R.74, B:H.75 PO4.12: 8 residues within 4Å: Chain C: G.31, T.32, R.74, H.75, T.107, A.108, T.211 Ligands: 7A6.11 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.32, C:T.107, C:A.108 Salt bridges: C:R.74, C:H.75

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: K.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.54, A:K.54 GOL.8: 1 residues within 4Å: Chain B: K.54 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.54, B:K.54 GOL.13: 1 residues within 4Å: Chain C: K.54 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.54, C:K.54

3 x NA: SODIUM ION(Non-functional Binders)

NA.4: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: NA.9, NA.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.132 NA.9: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: NA.4, NA.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.132 NA.14: 8 residues within 4Å: Chain A: T.132, M.133 Chain B: T.132, M.133 Chain C: T.132, M.133 Ligands: NA.4, NA.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.132

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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