MolNFT v1 · #25803 · protein
Proline racemase in complex with one molecule of pyrrole-2-carboxylic acid (hemi form)
1W62 · Proline racemase a: “Proline racemase in complex with one molecule of pyrrole-2-carboxylic acid (hemi form)”. X-ray diffraction, 1 ligand (PYC), 7 pockets (best druggability 0.75). MolNFT v1 #25803 on GenesisL1: 3D structure…
- PDB
- 1W62
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline racemase a
- EC
- 5.1.1.4
- UniProt
- Q4DA80
- Ligands
- PYC
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline racemase a (EC 5.1.1.4) | protein | 362 | 21% helix, 36% strand | Q4DA80 |
| B | Proline racemase a (EC 5.1.1.4) | protein | 351 | 19% helix, 38% strand | Q4DA80 |
Ligands and binding sites
- PYC · Pyrrole-2-carboxylate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.75 | 0.84 | 33 | empty |
| 2 | 424 | 0.69 | 0.81 | 55 | empty |
| 3 | 104 | 0.57 | 0.85 | 20 | empty |
| 4 | 79 | 0.41 | 0.78 | 18 | empty |
| 5 | 51 | 0.37 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1714 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1W62 · proline racemase in complex with one molecule of pyrrole-2-carboxylic acid (hemi form) · the same entry in another collection · chain A against A, TM-score 1.00
- Q4DA80 · AlphaFold monomer V2.0 prediction for proline racemase a (Q4DA80) · a predicted model of the same protein · chain A 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 Q4DA80
- Elsewhere: RCSB PDB 1W62 · PDBe 1W62 · UniProt Q4DA80
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