Research workbench
Carboxyethylarginine synthase from streptomyces clavuligerus: putative reaction intermediate complex
Analyse Carboxyethylarginine synthase from streptomyces clavuligerus: putative reaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IHU
- Type
- protein
- Length
- 2,216 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
- TP9, TP8, K, MG
- Pockets
- 20 · best druggability 0.78
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 | 562 | 43% helix, 17% strand | Q9LCV9 |
| B | Carboxyethylarginine synthase (EC 2.5.1.66) | protein | 552 | 42% helix, 17% strand | Q9LCV9 |
| C, D | Carboxyethylarginine synthase (EC 2.5.1.66) | protein | 551 | 41% helix, 17% strand | Q9LCV9 |
Ligands and binding sites
- TP9 · (3Z)-4-{[(4-amino-2-methylpyrimidin-5-yl)methyl]amino}-3-mercaptopent-3-en-1-yl trihydrogen diphosphate · ligand · 3 copies · chains A, B, C, D
- TP8 · 5-(2-{[hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-[(1Z)-1-hydroxy-3-(phosphonooxy)prop-1-en-1-yl]-3-{[(4Z)-4-imino-2- methyl-4,5-dihydropyrimidin-5-yl]methyl}-4-methyl-1,3-thiazol-3-ium · ligand · chains C, D
- K · Potassium ion · metal · 6 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- TAR · D(-)-tartaric acid · additive · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.78 | 0.87 | 62 | MG, TP9, TAR |
| 2 | 369 | 0.77 | 0.87 | 51 | MG, TP8 |
| 3 | 332 | 0.76 | 0.87 | 52 | MG, TP9 |
| 4 | 312 | 0.76 | 0.88 | 49 | MG, TP9, TAR |
| 5 | 251 | 0.73 | 0.88 | 53 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3699 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 3696 Ų buried · 53 hydrogen bonds · protein-protein
- B–D · 1055 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1033 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 261 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2IHU · Carboxyethylarginine synthase from Streptomyces clavuligerus: putative reaction… · 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 2IHU · PDBe 2IHU · UniProt Q9LCV9
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