MolNFT v1 · #55053 · protein
Crystal structure of mycobacterium tuberculosis phosphoribosyl isomerase with bound rcdrp
2Y85 · Phosphoribosyl isomerase a: “Crystal structure of mycobacterium tuberculosis phosphoribosyl isomerase with bound rcdrp”. X-ray diffraction, 3 ligands (137, NA, CL), 7 pockets (best druggability 0.88). MolNFT v1 #55053 on GenesisL1…
- PDB
- 2Y85
- Type
- protein
- Length
- 937 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosyl isomerase a
- EC
- 5.3.1.24, 5.3.1.16
- UniProt
- P60578
- Ligands
- 137, NA, CL
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosyl isomerase a (EC 5.3.1.24, 5.3.1.16) | protein | 234 | 38% helix, 25% strand | P60578 |
| B | Phosphoribosyl isomerase a (EC 5.3.1.24, 5.3.1.16) | protein | 236 | 39% helix, 26% strand | P60578 |
| C | Phosphoribosyl isomerase a (EC 5.3.1.24, 5.3.1.16) | protein | 233 | 39% helix, 25% strand | P60578 |
| D | Phosphoribosyl isomerase a (EC 5.3.1.24, 5.3.1.16) | protein | 234 | 40% helix, 27% strand | P60578 |
Ligands and binding sites
- 137 · 1-(O-carboxy-phenylamino)-1-deoxy-D-ribulose-5-phosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 11 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.88 | 0.89 | 130 | NA, 137, CL |
| 2 | 1084 | 0.76 | 0.78 | 97 | empty |
| 3 | 379 | 0.75 | 0.85 | 61 | NA, CL, 137 |
| 4 | 269 | 0.69 | 0.84 | 46 | NA, 137 |
| 5 | 63 | 0.47 | 0.84 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1123 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 455 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 312 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 188 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 183 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2Y85 · Crystal structure of mycobacterium tuberculosis phosphoribosyl isomerase with bound rcdrp · the same entry in another collection · chain A against A, TM-score 1.00
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 P60578
- Elsewhere: RCSB PDB 2Y85 · PDBe 2Y85 · UniProt P60578
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