Research workbench
Crystal structure of hypothetical protein (RV3272) from mycobacterium tuberculosis
Analyse Crystal structure of hypothetical protein (RV3272) from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YIT
- Type
- protein
- Length
- 1,753 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CoA transferase III
- UniProt
- P96877
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CoA transferase III | protein | 350 | 38% helix, 13% strand | P96877 |
| B | CoA transferase III | protein | 353 | 39% helix, 16% strand | P96877 |
| C | CoA transferase III | protein | 354 | 40% helix, 14% strand | P96877 |
| D | CoA transferase III | protein | 352 | 39% helix, 14% strand | P96877 |
| E | CoA transferase III | protein | 344 | 38% helix, 13% strand | P96877 |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.80 | 0.82 | 98 | empty |
| 2 | 749 | 0.73 | 0.78 | 91 | empty |
| 3 | 65 | 0.72 | 0.98 | 25 | empty |
| 4 | 624 | 0.67 | 0.77 | 63 | empty |
| 5 | 50 | 0.67 | 0.96 | 18 | empty |
Interfaces
7 interfaces between chains.
- C–D · 5771 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 5648 Ų buried · 78 hydrogen bonds · protein-protein
- C–E · 182 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 178 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5YIT · Crystal Structure of Hypothetical protein (Rv3272) from Mycobacterium tuberculosis · the same entry in another collection · chain E against E, 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 D against A, TM-score 0.98
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 5YIT · PDBe 5YIT · UniProt P96877
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