Research workbench
Apo structure of 4-hydroxy-tetrahydrodipicolinate reductase from mycobacterium tuberculosis
Analyse Apo structure of 4-hydroxy-tetrahydrodipicolinate reductase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TEK
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate reductase
- EC
- 1.17.1.8
- UniProt
- A5U6C6
- Ligands
- NA, CL
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 249 | 36% helix, 26% strand | A5U6C6 |
| B | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 247 | 36% helix, 26% strand | A5U6C6 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.61 | 0.78 | 34 | CL |
| 2 | 333 | 0.58 | 0.76 | 36 | CL |
| 3 | 191 | 0.50 | 0.77 | 23 | empty |
| 4 | 108 | 0.44 | 0.78 | 14 | empty |
| 5 | 106 | 0.36 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1312 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5TEK · Apo Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Mycobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- A5U6C6 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate reductase (A5U6C6) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 A5U6C6
- Elsewhere: RCSB PDB 5TEK · PDBe 5TEK · UniProt A5U6C6
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