Research workbench
Crystal structure of a putative uncharacterized protein RV3404C and likely sugar N-formyltransferase from mycobacterium tuberculosis bound to uridine diphosphate
Analyse Crystal structure of a putative uncharacterized protein RV3404C and likely… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q12
- Type
- protein
- Length
- 464 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein RV3404C/MT3512
- UniProt
- P65073
- Ligands
- UDP, CL
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein RV3404C/MT3512 | protein | 232 | 34% helix, 25% strand | P65073 |
| B | Uncharacterized protein RV3404C/MT3512 | protein | 232 | 35% helix, 25% strand | P65073 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.63 | 0.79 | 45 | UDP, EDO |
| 2 | 352 | 0.62 | 0.78 | 43 | UDP, EDO |
| 3 | 50 | 0.30 | 0.76 | 17 | EDO |
Interfaces
1 interface between chains.
- A–B · 1680 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 4Q12 · Crystal structure of a putative uncharacterized protein Rv3404c and likely sugar… · 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 P65073
- Elsewhere: RCSB PDB 4Q12 · PDBe 4Q12 · UniProt P65073
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