MolNFT v1 · #127309 · protein
Structure of the R domain of carboxylic acid reductase (car) from mycobacterium marinum in complex with NADP, P21 form
5MSU: “Structure of the R domain of carboxylic acid reductase (car) from mycobacterium marinum in complex with NADP…”. X-ray diffraction, 1 ligand (NAP), 9 pockets (best druggability 0.86). MolNFT v1 #127309 on GenesisL1: 3D structure…
- PDB
- 5MSU
- Type
- protein
- Length
- 1,329 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxylic acid reductase
- EC
- 1.2.1.-
- UniProt
- B2HN69
- Ligands
- NAP
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Carboxylic acid reductase (EC 1.2.1.-) | protein | 434 | 48% helix, 14% strand | B2HN69 |
| A | Carboxylic acid reductase (EC 1.2.1.-) | protein | 436 | 48% helix, 14% strand | B2HN69 |
| B | Carboxylic acid reductase (EC 1.2.1.-) | protein | 459 | 48% helix, 13% strand | B2HN69 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.86 | 0.87 | 128 | NAP |
| 2 | 864 | 0.74 | 0.78 | 70 | NAP |
| 3 | 276 | 0.61 | 0.79 | 42 | empty |
| 4 | 295 | 0.53 | 0.75 | 41 | empty |
| 5 | 53 | 0.42 | 0.83 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1080 Ų buried · 22 hydrogen bonds · protein-protein
- C–B · 330 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 105 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MSU · Structure of the R domain of carboxylic acid reductase (CAR) from Mycobacterium marinum… · the same entry in another collection · chain C against C, TM-score 1.00
- B2HN69 · AlphaFold monomer V2.0 prediction for carboxylic acid reductase (B2HN69) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 B2HN69
- Elsewhere: RCSB PDB 5MSU · PDBe 5MSU · UniProt B2HN69
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