Research workbench
Structure of gtpebb-dihydrobiliverdin complex
Analyse Structure of gtpebb-dihydrobiliverdin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QX6
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferredoxin bilin reductase plastid
- UniProt
- L1IWQ9
- Ligands
- DBV, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferredoxin bilin reductase plastid | protein | 264 | 44% helix, 20% strand | L1IWQ9 |
| B | Ferredoxin bilin reductase plastid | protein | 262 | 45% helix, 22% strand | L1IWQ9 |
Ligands and binding sites
- DBV · 15,16-dihydrobiliverdin · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.72 | 0.85 | 36 | DBV |
| 2 | 256 | 0.71 | 0.85 | 37 | DBV |
| 3 | 121 | 0.50 | 0.80 | 22 | empty |
| 4 | 159 | 0.47 | 0.76 | 28 | 1PE |
| 5 | 115 | 0.40 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 275 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6QX6 · Structure of gtPebB-dihydrobiliverdin complex · 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 L1IWQ9
- Elsewhere: RCSB PDB 6QX6 · PDBe 6QX6 · UniProt L1IWQ9
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