MolNFT v1 · #180917 · protein
Trimeric human arginase 1 in complex with MAB5
7LEY · Arginase-1: “Trimeric human arginase 1 in complex with MAB5”. Electron microscopy, 1 ligand (MN), 20 pockets (best druggability 0.78). MolNFT v1 #180917 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LEY
- Type
- protein
- Length
- 2,265 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase-1; MAB5 heavy chain; MAB5 light chain
- EC
- 3.5.3.1
- UniProt
- P05089
- Ligands
- MN
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 17% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Arginase-1 (EC 3.5.3.1) | protein | 317 | 36% helix, 16% strand | P05089 |
| D, G, H | MAB5 heavy chain | protein | 224 | 0% helix, 37% strand | — |
| E, F, I | MAB5 light chain | protein | 214 | 6% helix, 33% strand | — |
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
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.78 | 0.84 | 53 | empty |
| 2 | 342 | 0.67 | 0.81 | 47 | empty |
| 3 | 288 | 0.67 | 0.82 | 47 | empty |
| 4 | 298 | 0.66 | 0.82 | 45 | empty |
| 5 | 384 | 0.57 | 0.75 | 48 | empty |
Interfaces
12 interfaces between chains.
- F–G · 1983 Ų buried · 22 hydrogen bonds · protein-protein
- I–H · 1950 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1869 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 990 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 982 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
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 P05089
- Elsewhere: RCSB PDB 7LEY · PDBe 7LEY · UniProt P05089
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