MolNFT v1 · #127310 · protein
Structure of the phosphopantetheine modified pcp-R didomain of carboxylic acid reductase (car) in complex with NADP
5MSV · Thioester reductase domain-containing protein: “Structure of the phosphopantetheine modified pcp-R didomain of carboxylic acid reductase (car) in complex…”. X-ray diffraction, 2 ligands (PNS, NAP), 11 pockets (best druggability…
- PDB
- 5MSV
- Type
- protein
- Length
- 2,057 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioester reductase domain-containing protein
- UniProt
- E5XP76
- Ligands
- PNS, NAP
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioester reductase domain-containing protein | protein | 514 | 51% helix, 11% strand | E5XP76 |
| B | Thioester reductase domain-containing protein | protein | 514 | 51% helix, 11% strand | E5XP76 |
| C | Thioester reductase domain-containing protein | protein | 514 | 51% helix, 11% strand | E5XP76 |
| D | Thioester reductase domain-containing protein | protein | 515 | 50% helix, 11% strand | E5XP76 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · 4 copies · chains A, B, C, D
- 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.85 | 0.87 | 106 | PNS, NAP |
| 2 | 1078 | 0.85 | 0.86 | 107 | empty |
| 3 | 1158 | 0.84 | 0.85 | 117 | empty |
| 4 | 906 | 0.83 | 0.85 | 94 | PNS, NAP |
| 5 | 1180 | 0.82 | 0.83 | 106 | PNS, NAP |
Interfaces
3 interfaces between chains.
- B–D · 1030 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1023 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 802 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (phosphopantetheinylation).
Compared structures
- 5MSV · Structure of the phosphopantetheine modified PCP-R didomain of carboxylic acid reductase… · 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 C 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 5MSV · PDBe 5MSV · UniProt E5XP76
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