MolNFT v1 · #53039 · protein
Fluorescent protein killerred in the native state
2WIQ: “Fluorescent protein killerred in the native state”. X-ray diffraction, 3 ligands (CRQ, NA, SO4), 7 pockets (best druggability 0.80). MolNFT v1 #53039 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WIQ
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Killerred
- UniProt
- Q2TCH5
- Ligands
- CRQ, NA, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Killerred | protein | 225 | 7% helix, 53% strand | Q2TCH5 |
| B | Killerred | protein | 228 | 6% helix, 52% strand | Q2TCH5 |
Ligands and binding sites
- CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.80 | 0.98 | 34 | CRQ |
| 2 | 139 | 0.80 | 0.97 | 36 | CRQ |
| 3 | 105 | 0.47 | 0.80 | 27 | empty |
| 4 | 98 | 0.42 | 0.77 | 26 | empty |
| 5 | 72 | 0.35 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1459 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 2WIQ · Fluorescent protein KillerRed in the native state · 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
- Every structure of UniProt Q2TCH5
- Elsewhere: RCSB PDB 2WIQ · PDBe 2WIQ · UniProt Q2TCH5
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