MolNFT v1 · #146290 · protein
Crystal structure of bacterial (6-4) photolyase phrb from in situ serial laue diffraction
6DD6: “Crystal structure of bacterial (6-4) photolyase phrb from in situ serial laue diffraction”. X-ray diffraction, 3 ligands (FAD, DLZ, SF4), 5 pockets (best druggability 0.82). MolNFT v1 #146290 on GenesisL1: 3D structure, binding…
- PDB
- 6DD6
- Type
- protein
- Length
- 512 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photolyase phrb
- UniProt
- A0A083ZLV8
- Ligands
- FAD, DLZ, SF4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photolyase phrb | protein | 512 | 51% helix, 6% strand | A0A083ZLV8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- DLZ · 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol · ligand · chains A
- SF4 · Iron/sulfur cluster · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.82 | 0.85 | 82 | FAD |
| 2 | 144 | 0.81 | 0.97 | 23 | DLZ |
| 3 | 208 | 0.58 | 0.80 | 26 | empty |
| 4 | 90 | 0.52 | 0.84 | 31 | empty |
| 5 | 78 | 0.34 | 0.75 | 14 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6DD6 · Crystal structure of bacterial (6-4) photolyase PhrB from in situ serial Laue diffraction · 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 A0A083ZLV8
- Elsewhere: RCSB PDB 6DD6 · PDBe 6DD6 · UniProt A0A083ZLV8
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