Research workbench
Structural and functional importance of first-shell metal ligands in the binuclear manganese cluster of arginase I.
Analyse Structural and functional importance of first-shell metal ligands in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P8N
- Type
- protein
- Length
- 942 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase 1
- EC
- 3.5.3.1
- UniProt
- P07824
- Ligands
- MN
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Arginase 1 (EC 3.5.3.1) | protein | 314 | 41% helix, 16% strand | P07824 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.82 | 0.85 | 55 | empty |
| 2 | 231 | 0.56 | 0.78 | 33 | empty |
| 3 | 168 | 0.55 | 0.80 | 31 | empty |
| 4 | 124 | 0.54 | 0.82 | 22 | empty |
| 5 | 138 | 0.46 | 0.78 | 22 | GOL |
Interfaces
3 interfaces between chains.
- B–C · 1013 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 964 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 945 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1P8N · Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear… · the same entry in another collection · chain B against B, TM-score 1.00
- P07824 · AlphaFold monomer V2.0 prediction for arginase-1 (P07824) · a predicted model of the same protein · chain A 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 P07824
- Elsewhere: RCSB PDB 1P8N · PDBe 1P8N · UniProt P07824
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