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Crystal structure of fumarate hydratase class II from mycobacterium ulcerans in complex with L-malate
Analyse Crystal structure of fumarate hydratase class II from mycobacterium ulcerans in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T93
- Type
- protein
- Length
- 1,841 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
- A0PKR5
- Ligands
- LMR
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fumarate hydratase class II (EC 4.2.1.2) | protein | 461 | 62% helix, 9% strand | A0PKR5 |
| C | Fumarate hydratase class II (EC 4.2.1.2) | protein | 459 | 61% helix, 8% strand | A0PKR5 |
| D | Fumarate hydratase class II (EC 4.2.1.2) | protein | 460 | 60% helix, 8% strand | A0PKR5 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 6 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.82 | 0.97 | 25 | empty |
| 2 | 136 | 0.80 | 0.97 | 31 | empty |
| 3 | 137 | 0.78 | 0.96 | 30 | empty |
| 4 | 72 | 0.71 | 0.96 | 20 | empty |
| 5 | 66 | 0.70 | 0.96 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3505 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 3489 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 2973 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 2920 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 2145 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 7T93 · Crystal Structure of Fumarate hydratase class II from Mycobacterium ulcerans in complex… · 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 A0PKR5
- Elsewhere: RCSB PDB 7T93 · PDBe 7T93 · UniProt A0PKR5
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