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Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with butylthio-dadme-immucillin-a and chloride
Analyse Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TC5
- Type
- protein
- Length
- 825 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-methyl-5'-thioadenosine phosphorylase
- EC
- 2.4.2.28
- UniProt
- Q13126
- Ligands
- BIG, CL
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 286 | 30% helix, 24% strand | Q13126 |
| B | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 270 | 31% helix, 25% strand | Q13126 |
| C | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 269 | 32% helix, 26% strand | Q13126 |
Ligands and binding sites
- BIG · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol · ligand · 3 copies · chains A, C, B
- CL · Chloride ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.77 | 0.90 | 60 | CL |
| 2 | 561 | 0.75 | 0.82 | 53 | BIG, CL |
| 3 | 474 | 0.73 | 0.82 | 52 | BIG, CL |
| 4 | 598 | 0.73 | 0.80 | 54 | BIG, CL |
| 5 | 126 | 0.43 | 0.76 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1075 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1071 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1059 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5TC5 · Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13126 · AlphaFold monomer V2.0 prediction for S-methyl-5'-thioadenosine phosphorylase (Q13126) · a predicted model of the same protein · chain B against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q13126
- Elsewhere: RCSB PDB 5TC5 · PDBe 5TC5 · UniProt Q13126
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