MolNFT v1 · #118668 · protein
Fumarate hydratase of mycobacterium tuberculosis in complex with formate
5F92 · Fumarate hydratase class II: “Fumarate hydratase of mycobacterium tuberculosis in complex with formate”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.82). MolNFT v1 #118668 on GenesisL1: 3D structure, binding…
- PDB
- 5F92
- Type
- protein
- Length
- 1,830 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
- CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate hydratase class II (EC 4.2.1.2) | protein | 460 | 60% helix, 7% strand | P9WN92 |
| B | Fumarate hydratase class II (EC 4.2.1.2) | protein | 461 | 60% helix, 7% strand | P9WN92 |
| C | Fumarate hydratase class II (EC 4.2.1.2) | protein | 454 | 63% helix, 8% strand | P9WN92 |
| D | Fumarate hydratase class II (EC 4.2.1.2) | protein | 455 | 62% helix, 8% strand | P9WN92 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, D
- FMT · Formic acid · additive · 4 copies · chains A, C, D, B
- PG4 · Tetraethylene glycol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.82 | 0.98 | 24 | empty |
| 2 | 135 | 0.79 | 0.97 | 32 | empty |
| 3 | 124 | 0.78 | 0.97 | 32 | empty |
| 4 | 70 | 0.73 | 0.98 | 17 | empty |
| 5 | 68 | 0.69 | 0.96 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3547 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2806 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 2663 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2659 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 1820 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5F92 · Fumarate hydratase of Mycobacterium tuberculosis in complex with formate · 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 D 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 P9WN92
- Elsewhere: RCSB PDB 5F92 · PDBe 5F92 · UniProt P9WN92
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.