SMTL ID : 5tc5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-trimer

Ligands

3 x BIG: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol(Non-covalent)

BIG.1: 18 residues within 4Å: Chain A: P.83, A.108, C.109, G.110, I.186, F.191, I.208, N.209, M.210, T.233, D.234, D.236, V.250, L.251, L.254 Chain C: H.151, L.293 Ligands: CL.2 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:L.293, A:V.250, A:L.251, A:L.254 Hydrogen bonds: C:H.151, A:T.233, A:D.234, A:D.236, A:D.236 pi-Stacking: A:F.191 BIG.4: 17 residues within 4Å: Chain A: H.151, L.293 Chain B: 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, L.254 Ligands: CL.5 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.250, B:L.254, A:L.293 Hydrogen bonds: B:T.233, B:D.234, B:D.236, B:D.236, A:H.151 pi-Stacking: B:F.191 BIG.6: 17 residues within 4Å: Chain B: H.151, L.293 Chain C: P.83, A.108, C.109, G.110, I.186, F.191, I.208, N.209, M.210, T.233, D.234, D.236, V.250, L.251 Ligands: CL.7 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.251, B:L.293 Hydrogen bonds: C:D.234, C:D.234, B:H.151 pi-Stacking: C:F.191

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

CL.2: 5 residues within 4Å: Chain A: T.107, N.209, M.210, T.211 Ligands: BIG.1 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: R.130 Chain B: R.130 Chain C: R.130 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain B: T.107, N.209, M.210, T.211 Ligands: BIG.4 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain C: T.107, N.209, M.210, T.211 Ligands: BIG.6 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
B

C
C

S-methyl-5'-thioadenosine phosphorylase

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