MolNFT v1 · #28742 · protein
Crystal structure of N-succinylarginine dihydrolase, astb, bound to substrate and product, an enzyme from the arginine catabolic pathway of escherichia COLI
1YNH: “Crystal structure of N-succinylarginine dihydrolase, astb, bound to substrate and product, an enzyme from the…”. X-ray diffraction, 2 ligands (SUO, K), 20 pockets (best druggability 0.84). MolNFT v1 #28742 on GenesisL1: 3D…
- PDB
- 1YNH
- Type
- protein
- Length
- 1,757 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinylarginine dihydrolase
- EC
- 3.-.-.-
- UniProt
- P76216
- Ligands
- SUO, K
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Succinylarginine dihydrolase (EC 3.-.-.-) | protein | 439 | 41% helix, 19% strand | P76216 |
| B | Succinylarginine dihydrolase (EC 3.-.-.-) | protein | 440 | 41% helix, 20% strand | P76216 |
Ligands and binding sites
- SUO · N~2~-(3-carboxypropanoyl)-L-ornithine · ligand · 4 copies · chains A, B, C, D
- K · Potassium 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.84 | 0.85 | 103 | empty |
| 2 | 1035 | 0.75 | 0.77 | 71 | empty |
| 3 | 69 | 0.74 | 0.98 | 24 | empty |
| 4 | 70 | 0.73 | 0.98 | 23 | empty |
| 5 | 67 | 0.73 | 0.98 | 27 | empty |
Interfaces
5 interfaces between chains.
- B–C · 975 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 965 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 484 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 341 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 323 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1YNH · Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and… · the same entry in another collection · chain C against C, TM-score 1.00
- P76216 · AlphaFold monomer V2.0 prediction for N-succinylarginine dihydrolase (P76216) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P76216
- Elsewhere: RCSB PDB 1YNH · PDBe 1YNH · UniProt P76216
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