MolNFT v1 · #149485 · protein
Crystal structure of the photosensory core module (pcm) of a bathy phytochrome from agrobacterium fabrum in the pfr state.
6G1Y · Bacteriophytochrome protein: “Crystal structure of the photosensory core module (pcm) of a bathy phytochrome from agrobacterium fabrum in…”. X-ray diffraction, 1 ligand (EL5), 12 pockets (best druggability 0.83). MolNFT v1 #149485…
- PDB
- 6G1Y
- Type
- protein
- Length
- 985 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome protein
- UniProt
- A9CI81
- Ligands
- EL5
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome protein | protein | 492 | 40% helix, 22% strand | A9CI81 |
| B | Bacteriophytochrome protein | protein | 493 | 39% helix, 22% strand | A9CI81 |
Ligands and binding sites
- EL5 · Biliverdin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.83 | 0.91 | 45 | EL5 |
| 2 | 947 | 0.81 | 0.83 | 91 | EL5 |
| 3 | 1100 | 0.73 | 0.76 | 86 | empty |
| 4 | 524 | 0.62 | 0.75 | 46 | empty |
| 5 | 273 | 0.60 | 0.79 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 2 covalent (methylation, covalent ligand).
Compared structures
- 6G1Y · Crystal structure of the photosensory core module (PCM) of a bathy phytochrome from… · 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 A9CI81
- Elsewhere: RCSB PDB 6G1Y · PDBe 6G1Y · UniProt A9CI81
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