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The three-dimensional structure of N-succinyldiaminopimelate aminotransferase from mycobacterium tuberculosis
Analyse The three-dimensional structure of N-succinyldiaminopimelate aminotransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O0R
- Type
- protein
- Length
- 769 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RV0858C (N-succinyldiaminopimelate aminotransferase)
- EC
- 2.6.1.-
- UniProt
- O53870
- Ligands
- NA, CL
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RV0858C (N-succinyldiaminopimelate aminotransferase) (EC 2.6.1.-) | protein | 385 | 47% helix, 17% strand | O53870 |
| B | RV0858C (N-succinyldiaminopimelate aminotransferase) (EC 2.6.1.-) | protein | 384 | 47% helix, 17% strand | O53870 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.70 | 0.83 | 50 | GOL |
| 2 | 266 | 0.69 | 0.85 | 43 | GOL |
| 3 | 94 | 0.42 | 0.78 | 23 | empty |
| 4 | 86 | 0.41 | 0.78 | 16 | empty |
| 5 | 104 | 0.40 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2552 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 2O0R · The three-dimensional structure of N-Succinyldiaminopimelate aminotransferase from… · 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 O53870
- Elsewhere: RCSB PDB 2O0R · PDBe 2O0R · UniProt O53870
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