Research workbench
Crystal structure of RV3272 from M. tuberculosis orthorhombic form
Analyse Crystal structure of RV3272 from M. tuberculosis orthorhombic form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YX6
- Type
- protein
- Length
- 1,424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein RV3272
- UniProt
- P96877
- Ligands
- BEN
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein RV3272 | protein | 360 | 39% helix, 17% strand | P96877 |
| B | Uncharacterized protein RV3272 | protein | 356 | 41% helix, 15% strand | P96877 |
| C | Uncharacterized protein RV3272 | protein | 355 | 40% helix, 14% strand | P96877 |
| D | Uncharacterized protein RV3272 | protein | 353 | 40% helix, 16% strand | P96877 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.72 | 0.79 | 82 | empty |
| 2 | 54 | 0.71 | 0.98 | 17 | empty |
| 3 | 673 | 0.70 | 0.77 | 57 | GOL |
| 4 | 666 | 0.69 | 0.77 | 67 | GOL |
| 5 | 637 | 0.68 | 0.77 | 64 | empty |
Interfaces
4 interfaces between chains.
- A–B · 5750 Ų buried · 77 hydrogen bonds · protein-protein
- C–D · 5712 Ų buried · 73 hydrogen bonds · protein-protein
- B–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5YX6 · Crystal structure of Rv3272 from M. tuberculosis orthorhombic form · the same entry in another collection · chain D against D, TM-score 1.00
- P96877 · AlphaFold monomer V2.0 prediction for probable fatty acyl-CoA transferase RV3272 (P96877) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P96877
- Elsewhere: RCSB PDB 5YX6 · PDBe 5YX6 · UniProt P96877
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