MolNFT v1 · #127308 · protein
Structure of the a domain of carboxylic acid reductase (car) from segniliparus rugosus in complex with AMP and a co-purified carboxylic acid
5MST · Thioester reductase domain-containing protein: “Structure of the a domain of carboxylic acid reductase (car) from segniliparus rugosus in complex with AMP…”. X-ray diffraction, 3 ligands (FUM, AMP, CA), 17 pockets (best druggability…
- PDB
- 5MST
- Type
- protein
- Length
- 1,263 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioester reductase domain-containing protein
- UniProt
- E5XP76
- Ligands
- FUM, AMP, CA
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioester reductase domain-containing protein | protein | 631 | 40% helix, 25% strand | E5XP76 |
| B | Thioester reductase domain-containing protein | protein | 632 | 40% helix, 24% strand | E5XP76 |
Ligands and binding sites
- FUM · Fumaric acid · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.84 | 0.87 | 88 | FUM, AMP |
| 2 | 1137 | 0.82 | 0.83 | 124 | FUM, AMP |
| 3 | 592 | 0.79 | 0.84 | 56 | empty |
| 4 | 275 | 0.75 | 0.88 | 38 | empty |
| 5 | 300 | 0.74 | 0.87 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 858 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5MST · Structure of the A domain of carboxylic acid reductase (CAR) from Segniliparus rugosus in… · the same entry in another collection · chain A against A, TM-score 1.00
- E5XP76 · AlphaFold monomer V2.0 prediction for carboxylic acid reductase (E5XP76) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 E5XP76
- Elsewhere: RCSB PDB 5MST · PDBe 5MST · UniProt E5XP76
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