MolNFT v1 · #25606 · protein
The high resolution structure of mycobacterium tuberculosis leub (RV2995C)
1W0D · 3-isopropylmalate dehydrogenase: “The high resolution structure of mycobacterium tuberculosis leub (RV2995C)”. X-ray diffraction, 1 ligand (SO4), 15 pockets (best druggability 0.75). MolNFT v1 #25606 on GenesisL1: 3D structure…
- PDB
- 1W0D
- Type
- protein
- Length
- 1,348 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-isopropylmalate dehydrogenase
- EC
- 1.1.1.85
- UniProt
- P95313
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 337 | 45% helix, 21% strand | P95313 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.75 | 0.99 | 22 | empty |
| 2 | 525 | 0.74 | 0.82 | 44 | empty |
| 3 | 56 | 0.73 | 0.99 | 23 | empty |
| 4 | 452 | 0.71 | 0.81 | 43 | empty |
| 5 | 485 | 0.71 | 0.81 | 45 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 2153 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2117 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 516 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1W0D · The high resolution structure of Mycobacterium tuberculosis LeuB (Rv2995c) · 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 P95313
- Elsewhere: RCSB PDB 1W0D · PDBe 1W0D · UniProt P95313
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