Research workbench
Crystal structure of circular-permutated mkate
Analyse Crystal structure of circular-permutated mkate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RWA
- Type
- protein
- Length
- 1,856 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein FP480
- UniProt
- D0VX33
- Ligands
- NRQ
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Fluorescent protein FP480 | protein | 232 | 6% helix, 53% strand | D0VX33 |
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 · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.84 | 0.86 | 108 | empty |
| 2 | 1178 | 0.83 | 0.84 | 114 | empty |
| 3 | 98 | 0.77 | 0.98 | 27 | NRQ |
| 4 | 94 | 0.77 | 0.98 | 26 | NRQ |
| 5 | 89 | 0.76 | 0.98 | 27 | NRQ |
Interfaces
13 interfaces between chains.
- C–F · 1538 Ų buried · 28 hydrogen bonds · protein-protein
- D–G · 1531 Ų buried · 32 hydrogen bonds · protein-protein
- E–H · 1505 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1504 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 978 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 3RWA · Crystal structure of circular-permutated mKate · 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 D0VX33
- Elsewhere: RCSB PDB 3RWA · PDBe 3RWA · UniProt D0VX33
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