MolNFT v1 · #161311 · protein
Crystal structure of human arginase-1 at pH 9.0 in complex with cb- 1158/INCB001158
6QAF: “Crystal structure of human arginase-1 at pH 9.0 in complex with cb- 1158/INCB001158”. X-ray diffraction, 3 ligands (XC3, MN, NA), 6 pockets (best druggability 0.73). MolNFT v1 #161311 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6QAF
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase-1
- EC
- 3.5.3.1
- UniProt
- P05089
- Ligands
- XC3, MN, NA
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Arginase-1 (EC 3.5.3.1) | protein | 318 | 44% helix, 16% strand | P05089 |
Ligands and binding sites
- XC3 · [(~{E})-3-[(3~{S},4~{R})-4-azanyl-1-[(2~{S})-2-azanylpropanoyl]-4-carboxy-pyrrolidin-3-yl]prop-1-enyl]-tris(oxidanyl)boranium · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.73 | 0.84 | 40 | empty |
| 2 | 638 | 0.67 | 0.76 | 71 | XC3 |
| 3 | 93 | 0.43 | 0.79 | 21 | XC3 |
| 4 | 55 | 0.37 | 0.80 | 14 | empty |
| 5 | 52 | 0.36 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 480 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6QAF · Crystal structure of human Arginase-1 at pH 9.0 in complex with CB-1158/INCB001158 · the same entry in another collection · chain A against A, TM-score 1.00
- P05089 · AlphaFold monomer V2.0 prediction for arginase-1 (P05089) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 6QAF · PDBe 6QAF · UniProt P05089
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