Research workbench
Crystal structure of ilvd from mycobacterium tuberculosis
Analyse Crystal structure of ilvd from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OVT
- Type
- protein
- Length
- 2,235 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroxy-acid dehydratase
- EC
- 4.2.1.9
- UniProt
- A0A0E8UWV6
- Ligands
- FES, MG, NA
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroxy-acid dehydratase (EC 4.2.1.9) | protein | 562 | 41% helix, 15% strand | A0A0E8UWV6 |
| B | Dihydroxy-acid dehydratase (EC 4.2.1.9) | protein | 555 | 41% helix, 16% strand | A0A0E8UWV6 |
| C | Dihydroxy-acid dehydratase (EC 4.2.1.9) | protein | 558 | 41% helix, 16% strand | A0A0E8UWV6 |
| D | Dihydroxy-acid dehydratase (EC 4.2.1.9) | protein | 560 | 42% helix, 17% strand | A0A0E8UWV6 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.87 | 0.89 | 105 | MG |
| 2 | 232 | 0.83 | 0.96 | 64 | FES |
| 3 | 107 | 0.80 | 0.98 | 18 | empty |
| 4 | 108 | 0.80 | 0.98 | 18 | empty |
| 5 | 919 | 0.80 | 0.82 | 129 | FES |
Interfaces
6 interfaces between chains.
- A–C · 3622 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 3522 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 790 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 788 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 655 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6OVT · Crystal Structure of IlvD from Mycobacterium tuberculosis · 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 A0A0E8UWV6
- Elsewhere: RCSB PDB 6OVT · PDBe 6OVT · UniProt A0A0E8UWV6
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