Research workbench
Crystal structure of M. tuberculosis yefm antitoxin
Analyse Crystal structure of M. tuberculosis yefm antitoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D55
- Type
- protein
- Length
- 320 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein RV3357/MT3465
- UniProt
- P65067
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein RV3357/MT3465 | protein | 68 | 60% helix, 18% strand | P65067 |
| B | Uncharacterized protein RV3357/MT3465 | protein | 84 | 62% helix, 17% strand | P65067 |
| C | Uncharacterized protein RV3357/MT3465 | protein | 86 | 67% helix, 14% strand | P65067 |
| D | Uncharacterized protein RV3357/MT3465 | protein | 82 | 62% helix, 13% strand | P65067 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.35 | 0.76 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1353 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1310 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1289 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 968 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 417 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3D55 · Crystal structure of M. tuberculosis YefM antitoxin · 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 P65067
- Elsewhere: RCSB PDB 3D55 · PDBe 3D55 · UniProt P65067
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