MolNFT v1 · #40167 · protein
Carboxyethylarginine synthase from streptomyces clavuligerus: 5- guanidinovaleric acid complex
2IHV: “Carboxyethylarginine synthase from streptomyces clavuligerus: 5- guanidinovaleric acid complex”. X-ray diffraction, 4 ligands (TPP, GVA, K), 20 pockets (best druggability 0.80). MolNFT v1 #40167 on GenesisL1: 3D structure, binding…
- PDB
- 2IHV
- Type
- protein
- Length
- 2,240 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, GVA, K, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Carboxyethylarginine synthase (EC 2.5.1.66) | protein | 563 | 42% helix, 17% strand | Q9LCV9 |
| C | Carboxyethylarginine synthase (EC 2.5.1.66) | protein | 551 | 42% helix, 17% strand | Q9LCV9 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, C, D
- GVA · 5-{[amino(imino)methyl]amino}pentanoic acid · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 6 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.80 | 0.90 | 57 | MG, TPP, GVA |
| 2 | 322 | 0.79 | 0.90 | 54 | MG, TPP, GVA |
| 3 | 362 | 0.79 | 0.89 | 56 | MG, TPP, GVA |
| 4 | 311 | 0.76 | 0.88 | 47 | MG, TPP, GVA |
| 5 | 314 | 0.69 | 0.83 | 50 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3968 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 3877 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 1039 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1031 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 254 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2IHV · Carboxyethylarginine synthase from Streptomyces clavuligerus: 5-guanidinovaleric acid… · 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 2IHV · PDBe 2IHV · UniProt Q9LCV9
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