MolNFT v1 · #168381 · protein
CRIMSON 0.9
6WEM · Mcrimson 0.9: “CRIMSON 0.9”. X-ray diffraction, 1 ligand (NRQ), 10 pockets (best druggability 0.83). MolNFT v1 #168381 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WEM
- Type
- protein
- Length
- 890 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mcrimson 0.9
- Ligands
- NRQ
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mcrimson 0.9 | protein | 224 | 6% helix, 56% strand | — |
| B | Mcrimson 0.9 | protein | 223 | 8% helix, 56% strand | — |
| C | Mcrimson 0.9 | protein | 222 | 8% helix, 56% strand | — |
| D | Mcrimson 0.9 | protein | 221 | 8% helix, 57% strand | — |
Ligands and binding sites
- NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.83 | 0.84 | 117 | empty |
| 2 | 88 | 0.76 | 0.98 | 30 | NRQ |
| 3 | 85 | 0.76 | 0.98 | 26 | NRQ |
| 4 | 64 | 0.72 | 0.98 | 22 | NRQ |
| 5 | 57 | 0.70 | 0.97 | 22 | NRQ |
Interfaces
6 interfaces between chains.
- A–B · 1566 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1392 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 896 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 859 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 76 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 6WEM · Crimson 0.9 · the same entry in another collection · 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
- Elsewhere: RCSB PDB 6WEM · PDBe 6WEM
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