Research workbench
Fumarate hydratase of mycobacterium tuberculosis in complex with formate and allosteric modulator N-(2-methoxy-5-((1,2,4,5-tetrahydro- 3H-BENZO[D]AZEPIN-3-YL)SULFONYL)PHENYL)-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
- 6S88
- Type
- protein
- Length
- 1,807 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
- A0A045IXZ8
- Ligands
- L0K, MG
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate hydratase class II (EC 4.2.1.2) | protein | 450 | 62% helix, 7% strand | A0A045IXZ8 |
| B | Fumarate hydratase class II (EC 4.2.1.2) | protein | 458 | 60% helix, 7% strand | A0A045IXZ8 |
| C | Fumarate hydratase class II (EC 4.2.1.2) | protein | 451 | 63% helix, 8% strand | A0A045IXZ8 |
| D | Fumarate hydratase class II (EC 4.2.1.2) | protein | 448 | 61% helix, 8% strand | A0A045IXZ8 |
Ligands and binding sites
- L0K · ~{N}-[2-methoxy-5-(1,2,4,5-tetrahydro-3-benzazepin-3-ylsulfonyl)phenyl]-2-(4-oxidanylidene-3~{H}-phthalazin-1-yl)ethanamide · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains 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 | 145 | 0.82 | 0.98 | 24 | empty |
| 2 | 131 | 0.79 | 0.97 | 33 | empty |
| 3 | 124 | 0.78 | 0.97 | 31 | empty |
| 4 | 992 | 0.76 | 0.78 | 96 | empty |
| 5 | 69 | 0.73 | 0.98 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2918 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2827 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2527 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 2120 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1646 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6S88 · Fumarate hydratase of Mycobacterium tuberculosis in complex with formate and allosteric… · 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 A0A045IXZ8
- Elsewhere: RCSB PDB 6S88 · PDBe 6S88 · UniProt A0A045IXZ8
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