MolNFT v1 · #179403 · protein
Human arginase 1 in complex with compound 01.
7K4G · Arginase-1: “Human arginase 1 in complex with compound 01.”. X-ray diffraction, 2 ligands (VUV, MN), 20 pockets (best druggability 0.80). MolNFT v1 #179403 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7K4G
- Type
- protein
- Length
- 1,905 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase-1
- EC
- 3.5.3.1
- UniProt
- P05089
- Ligands
- VUV, MN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Arginase-1 (EC 3.5.3.1) | protein | 317 | 42% helix, 15% strand | P05089 |
| B | Arginase-1 (EC 3.5.3.1) | protein | 318 | 42% helix, 15% strand | P05089 |
| D | Arginase-1 (EC 3.5.3.1) | protein | 318 | 42% helix, 15% strand | P05089 |
| E | Arginase-1 (EC 3.5.3.1) | protein | 319 | 40% helix, 15% strand | P05089 |
| F | Arginase-1 (EC 3.5.3.1) | protein | 316 | 40% helix, 16% strand | P05089 |
Ligands and binding sites
- VUV · 3-[(2~{S},3~{R})-2-carboxypyrrolidin-3-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boranuide · ligand · 6 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 12 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.80 | 0.82 | 97 | empty |
| 2 | 786 | 0.79 | 0.83 | 65 | empty |
| 3 | 226 | 0.57 | 0.79 | 38 | empty |
| 4 | 213 | 0.54 | 0.78 | 32 | empty |
| 5 | 191 | 0.54 | 0.78 | 29 | empty |
Interfaces
8 interfaces between chains.
- C–F · 1024 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 1015 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 1015 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1012 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1004 Ų buried · 23 hydrogen bonds · protein-protein
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 7K4G · PDBe 7K4G · UniProt P05089
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