Research workbench
Structure of the fluorescent protein CMFP512 at 1.35A from cerianthus membranaceus
Analyse Structure of the fluorescent protein CMFP512 at 1.35A from cerianthus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C9J
- Type
- protein
- Length
- 1,732 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein FP512
- UniProt
- Q5ZQQ5
- Ligands
- CRQ
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein FP512 | protein | 213 | 4% helix, 57% strand | Q5ZQQ5 |
| B, C | Green fluorescent protein FP512 | protein | 217 | 6% helix, 56% strand | Q5ZQQ5 |
| D, H | Green fluorescent protein FP512 | protein | 218 | 5% helix, 56% strand | Q5ZQQ5 |
| E, G | Green fluorescent protein FP512 | protein | 217 | 5% helix, 56% strand | Q5ZQQ5 |
| F | Green fluorescent protein FP512 | protein | 215 | 4% helix, 57% strand | Q5ZQQ5 |
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 · 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
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.82 | 0.83 | 109 | empty |
| 2 | 739 | 0.82 | 0.86 | 81 | empty |
| 3 | 66 | 0.74 | 0.98 | 28 | CRQ |
| 4 | 57 | 0.73 | 0.99 | 25 | CRQ |
| 5 | 61 | 0.72 | 0.98 | 26 | CRQ |
Interfaces
14 interfaces between chains.
- G–H · 1733 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1709 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1660 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1579 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1411 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 2C9J · Structure of the fluorescent protein cmFP512 at 1.35A from Cerianthus membranaceus · 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 Q5ZQQ5
- Elsewhere: RCSB PDB 2C9J · PDBe 2C9J · UniProt Q5ZQQ5
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