Research workbench
Fumarate hydratase of mycobacterium tuberculosis in complex with formate and allosteric modulator (N-(5-(azepan-1-ylsulfonyl)-2- methoxyphenyl)-2-(4-oxo-3,4-dihydrophthalazin-1-YL)ACETAMIDE)
Analyse Fumarate hydratase of mycobacterium tuberculosis in complex with formate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F91
- Type
- protein
- Length
- 1,787 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate hydratase class II
- EC
- 4.2.1.2
- UniProt
- P9WN92
- Ligands
- 5WJ, CL
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate hydratase class II (EC 4.2.1.2) | protein | 447 | 62% helix, 8% strand | P9WN92 |
| B | Fumarate hydratase class II (EC 4.2.1.2) | protein | 452 | 61% helix, 7% strand | P9WN92 |
| C | Fumarate hydratase class II (EC 4.2.1.2) | protein | 448 | 63% helix, 8% strand | P9WN92 |
| D | Fumarate hydratase class II (EC 4.2.1.2) | protein | 440 | 62% helix, 5% strand | P9WN92 |
Ligands and binding sites
- 5WJ · ~{N}-[5-(azepan-1-ylsulfonyl)-2-methoxy-phenyl]-2-(4-oxidanylidene-3~{H}-phthalazin-1-yl)ethanamide · ligand · 2 copies · chains A, C
- CL · Chloride ion · ion · 5 copies · chains A, B, D
- FMT · Formic acid · additive · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.82 | 0.98 | 26 | empty |
| 2 | 122 | 0.78 | 0.97 | 31 | empty |
| 3 | 116 | 0.78 | 0.98 | 32 | empty |
| 4 | 952 | 0.77 | 0.80 | 91 | FMT |
| 5 | 67 | 0.73 | 0.98 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2942 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2831 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2504 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 2098 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1621 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5F91 · Fumarate hydratase of Mycobacterium tuberculosis in complex with formate and allosteric… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WN92 · AlphaFold monomer V2.0 prediction for fumarate hydratase class II (P9WN92) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P9WN92
- Elsewhere: RCSB PDB 5F91 · PDBe 5F91 · UniProt P9WN92
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