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Structures of dhbn domain of gallus gallus blm helicase
Analyse Structures of dhbn domain of gallus gallus blm helicase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LUT
- Type
- protein
- Length
- 530 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blm helicase
- UniProt
- Q5ZJM1
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 8 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Blm helicase | protein | 52 | 79% helix, 0% strand | Q5ZJM1 |
| B | Blm helicase | protein | 53 | 75% helix, 0% strand | Q5ZJM1 |
| D | Blm helicase | protein | 54 | 76% helix, 0% strand | Q5ZJM1 |
| F | Blm helicase | protein | 55 | 73% helix, 0% strand | Q5ZJM1 |
| H | Blm helicase | protein | 50 | 68% helix, 0% strand | Q5ZJM1 |
| I | Blm helicase | protein | 48 | 71% helix, 0% strand | Q5ZJM1 |
| J | Blm helicase | protein | 40 | 30% helix, 0% strand | Q5ZJM1 |
| K | Blm helicase | protein | 22 | 68% helix, 0% strand | Q5ZJM1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains B, C, D, E, A, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.54 | 0.84 | 23 | empty |
| 2 | 123 | 0.53 | 0.82 | 27 | empty |
| 3 | 87 | 0.52 | 0.84 | 21 | empty |
| 4 | 117 | 0.51 | 0.81 | 21 | empty |
| 5 | 183 | 0.46 | 0.75 | 31 | empty |
Interfaces
18 interfaces between chains.
- C–D · 1418 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1409 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 1405 Ų buried · 6 hydrogen bonds · protein-protein
- H–I · 1370 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 521 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 5LUT · Structures of DHBN domain of Gallus gallus BLM helicase · 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 Q5ZJM1
- Elsewhere: RCSB PDB 5LUT · PDBe 5LUT · UniProt Q5ZJM1
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