Research workbench
Carboxyethylarginine synthase from streptomyces clavuligerus (semet structure)
Analyse Carboxyethylarginine synthase from streptomyces clavuligerus (semet structure) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UPA
- Type
- protein
- Length
- 2,222 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxyethylarginine synthase
- UniProt
- Q9LCV9
- Ligands
- TPP, MG, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Carboxyethylarginine synthase | protein | 558 | 42% helix, 17% strand | Q9LCV9 |
| B | Carboxyethylarginine synthase | protein | 559 | 43% helix, 17% strand | Q9LCV9 |
| C | Carboxyethylarginine synthase | protein | 547 | 42% helix, 17% strand | Q9LCV9 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.83 | 0.84 | 156 | empty |
| 2 | 300 | 0.80 | 0.91 | 53 | TPP, MG, SO4 |
| 3 | 351 | 0.80 | 0.90 | 54 | TPP, MG, SO4 |
| 4 | 382 | 0.79 | 0.88 | 61 | TPP, MG, SO4 |
| 5 | 582 | 0.77 | 0.84 | 69 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3725 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3725 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1076 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1045 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 262 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 1UPA · Carboxyethylarginine synthase from Streptomyces clavuligerus (SeMet structure) · the same entry in another collection · chain D against D, TM-score 1.00
- Q9LCV9 · AlphaFold monomer V2.0 prediction for N(2)-(2-CARBOXYETHYL)ARGININE synthase (Q9LCV9) · a predicted model of the same protein · chain C 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 Q9LCV9
- Elsewhere: RCSB PDB 1UPA · PDBe 1UPA · UniProt Q9LCV9
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