Research workbench
Crystal structure of N-succinylarginine dihydrolase, astb, bound to substrate and product, an enzyme from the arginine catabolic pathway of escherichia COLI
Analyse Crystal structure of N-succinylarginine dihydrolase, astb, bound to substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YNF
- Type
- protein
- Length
- 2,574 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinylarginine dihydrolase
- EC
- 3.-.-.-
- UniProt
- P76216
- Ligands
- K
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Succinylarginine dihydrolase (EC 3.-.-.-) | protein | 429 | 41% helix, 20% strand | P76216 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.75 | 0.98 | 35 | empty |
| 2 | 85 | 0.75 | 0.98 | 33 | empty |
| 3 | 69 | 0.74 | 0.98 | 26 | empty |
| 4 | 68 | 0.73 | 0.98 | 25 | empty |
| 5 | 55 | 0.73 | 0.99 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–F · 932 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 916 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 915 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 569 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 441 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified (engineered).
Compared structures
- 1YNF · Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and… · the same entry in another collection · chain F against F, 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 1YNF · PDBe 1YNF · UniProt P76216
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