MolNFT v1 · #40165 · protein
Carboxyethylarginine synthase from streptomyces clavuligerus: semet structure
2IHT: “Carboxyethylarginine synthase from streptomyces clavuligerus: semet structure”. X-ray diffraction, 3 ligands (TPP, MG, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #40165 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2IHT
- Type
- protein
- Length
- 2,239 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxyethylarginine synthase
- EC
- 2.5.1.66
- UniProt
- Q9LCV9
- Ligands
- TPP, MG, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxyethylarginine synthase (EC 2.5.1.66) | protein | 560 | 42% helix, 17% strand | Q9LCV9 |
| B | Carboxyethylarginine synthase (EC 2.5.1.66) | protein | 561 | 43% helix, 17% strand | Q9LCV9 |
| C, D | Carboxyethylarginine synthase (EC 2.5.1.66) | protein | 559 | 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
- GOL · Glycerol · additive · 4 copies · chains A, B, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.82 | 0.95 | 48 | MG, SO4, TPP |
| 2 | 401 | 0.79 | 0.88 | 64 | MG, SO4, TPP |
| 3 | 353 | 0.79 | 0.89 | 60 | MG, SO4, TPP |
| 4 | 386 | 0.78 | 0.88 | 64 | MG, SO4, TPP |
| 5 | 278 | 0.73 | 0.87 | 56 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3815 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3803 Ų buried · 57 hydrogen bonds · protein-protein
- B–D · 1067 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1043 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 266 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 2IHT · 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 B 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 2IHT · PDBe 2IHT · UniProt Q9LCV9
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