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Structures of DHBN domain of human BLM helicase
Analyse Structures of DHBN domain of human BLM helicase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MK5
- Type
- protein
- Length
- 203 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.16
- Source
- Homo sapiens
- Molecule
- Bloom syndrome protein
- EC
- 3.6.4.12
- UniProt
- P54132
- Ligands
- K, IOD
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · resolution 2.16 · 3 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bloom syndrome protein (EC 3.6.4.12) | protein | 51 | 76% helix, 0% strand | P54132 |
| B, C | Bloom syndrome protein (EC 3.6.4.12) | protein | 52 | 79% helix, 0% strand | P54132 |
| D | Bloom syndrome protein (EC 3.6.4.12) | protein | 48 | 79% helix, 0% strand | P54132 |
Ligands and binding sites
- K · Potassium ion · metal · 3 copies · chains A, C
- IOD · Iodide ion · ion · 20 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.39 | 0.75 | 22 | IOD |
| 2 | 61 | 0.28 | 0.72 | 13 | IOD |
Interfaces
5 interfaces between chains.
- A–B · 1330 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 1299 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 189 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 148 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 134 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P54132
- Elsewhere: RCSB PDB 5MK5 · PDBe 5MK5 · UniProt P54132
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