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Crystal structure of fumarasec (S319C) from mannheimia succiniciproducens in complex with malate
Analyse Crystal structure of fumarasec (S319C) from mannheimia succiniciproducens in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C1A
- Type
- protein
- Length
- 1,846 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
- Q65UJ3
- Ligands
- LMR
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Fumarate hydratase class II (EC 4.2.1.2) | protein | 462 | 61% helix, 8% strand | Q65UJ3 |
| D | Fumarate hydratase class II (EC 4.2.1.2) | protein | 460 | 62% helix, 8% strand | Q65UJ3 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.70 | 0.80 | 37 | empty |
| 2 | 548 | 0.70 | 0.79 | 41 | empty |
| 3 | 139 | 0.67 | 0.88 | 29 | empty |
| 4 | 51 | 0.66 | 0.96 | 17 | empty |
| 5 | 175 | 0.64 | 0.85 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3702 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 3601 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 2807 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2801 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 2184 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7C1A · Crystal structure of FumaraseC (S319C) from Mannheimia succiniciproducens in complex with… · 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 Q65UJ3
- Elsewhere: RCSB PDB 7C1A · PDBe 7C1A · UniProt Q65UJ3
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