Research workbench
Carboxymethylproline synthase (carb) from pectobacterium carotovora, complexed with acetyl CoA and bicine
Analyse Carboxymethylproline synthase (carb) from pectobacterium carotovora, complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A81
- Type
- protein
- Length
- 697 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carb
- UniProt
- Q9XB60
- Ligands
- ACO, BCN
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carb | protein | 235 | 54% helix, 17% strand | Q9XB60 |
| B, C | Carb | protein | 231 | 52% helix, 17% strand | Q9XB60 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.77 | 0.79 | 104 | empty |
| 2 | 68 | 0.71 | 0.96 | 19 | empty |
| 3 | 219 | 0.70 | 0.86 | 30 | empty |
| 4 | 195 | 0.67 | 0.86 | 31 | BCN |
| 5 | 89 | 0.44 | 0.79 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 982 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 967 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 813 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2A81 · carboxymethylproline synthase (CarB) from pectobacterium carotovora, complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XB60 · AlphaFold monomer V2.0 prediction for carboxymethylproline synthase (Q9XB60) · 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 Q9XB60
- Elsewhere: RCSB PDB 2A81 · PDBe 2A81 · UniProt Q9XB60
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