Research workbench
Structure and mapping of spontaneous mutational sites of pyrr from mycobacterium tuberculosis
Analyse Structure and mapping of spontaneous mutational sites of pyrr from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IAO
- Type
- protein
- Length
- 1,026 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein pyrr
- EC
- 2.4.2.9
- UniProt
- A5U281
- Ligands
- URF
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Bifunctional protein pyrr (EC 2.4.2.9) | protein | 171 | 31% helix, 29% strand | A5U281 |
Ligands and binding sites
- URF · 5-fluorouracil · ligand · 3 copies · chains A, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.74 | 0.78 | 90 | empty |
| 2 | 57 | 0.53 | 0.88 | 11 | empty |
| 3 | 179 | 0.52 | 0.78 | 24 | empty |
| 4 | 266 | 0.50 | 0.74 | 36 | empty |
| 5 | 108 | 0.48 | 0.80 | 19 | empty |
Interfaces
6 interfaces between chains.
- E–F · 917 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 897 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 896 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 522 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 491 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5IAO · Structure and mapping of spontaneous mutational sites of PyrR from Mycobacterium… · the same entry in another collection · chain C against C, TM-score 1.00
- A5U281 · AlphaFold monomer V2.0 prediction for bifunctional protein pyrr (A5U281) · a predicted model of the same protein · chain A 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 A5U281
- Elsewhere: RCSB PDB 5IAO · PDBe 5IAO · UniProt A5U281
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