MolNFT v1 · #127306 · protein
Structure of the unmodified pcp-R domain of carboxylic acid reductase (car) from segniliparus rugosus in complex with NADPH, P43 form
5MSR · Thioester reductase domain-containing protein: “Structure of the unmodified pcp-R domain of carboxylic acid reductase (car) from segniliparus rugosus in…”. X-ray diffraction, 1 ligand (NAP), 11 pockets (best druggability 0.85).…
- PDB
- 5MSR
- Type
- protein
- Length
- 2,054 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioester reductase domain-containing protein
- UniProt
- E5XP76
- Ligands
- NAP
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioester reductase domain-containing protein | protein | 514 | 48% helix, 11% strand | E5XP76 |
| B | Thioester reductase domain-containing protein | protein | 520 | 48% helix, 11% strand | E5XP76 |
| C | Thioester reductase domain-containing protein | protein | 516 | 48% helix, 11% strand | E5XP76 |
| D | Thioester reductase domain-containing protein | protein | 504 | 49% helix, 11% strand | E5XP76 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.85 | 0.86 | 79 | empty |
| 2 | 1100 | 0.85 | 0.86 | 92 | empty |
| 3 | 1137 | 0.83 | 0.84 | 128 | empty |
| 4 | 982 | 0.79 | 0.80 | 77 | NAP |
| 5 | 995 | 0.79 | 0.80 | 82 | NAP |
Interfaces
5 interfaces between chains.
- B–D · 773 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 741 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 343 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 254 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 165 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MSR · Structure of the unmodified PCP-R domain of carboxylic acid reductase (CAR) from… · the same entry in another collection · chain D against D, TM-score 1.00
- E5XP76 · AlphaFold monomer V2.0 prediction for carboxylic acid reductase (E5XP76) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 5MSR · PDBe 5MSR · UniProt E5XP76
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