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
- 1P8M
- 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
- 11 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Arginase 1 (EC 3.5.3.1) | protein | 314 | 42% helix, 17% strand | P07824 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.81 | 0.84 | 59 | empty |
| 2 | 212 | 0.59 | 0.80 | 31 | empty |
| 3 | 224 | 0.55 | 0.78 | 30 | empty |
| 4 | 139 | 0.52 | 0.80 | 18 | empty |
| 5 | 71 | 0.46 | 0.82 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 996 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 961 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 945 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1P8M · Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear… · the same entry in another collection · chain A against A, TM-score 1.00
- P07824 · AlphaFold monomer V2.0 prediction for arginase-1 (P07824) · 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 P07824
- Elsewhere: RCSB PDB 1P8M · PDBe 1P8M · UniProt P07824
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