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Structure of an engineered helicase domain construct for human bloom syndrome protein (blm)
Analyse Structure of an engineered helicase domain construct for human bloom syndrome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AUD
- Type
- protein + DNA
- Length
- 3,165 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bloom syndrome PROTEIN,BLOOM syndrome protein; DNA…
- EC
- 3.6.4.12
- UniProt
- P54132
- Ligands
- ADP, RY8, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bloom syndrome PROTEIN,BLOOM syndrome protein (EC 3.6.4.12) | protein | 522 | 49% helix, 12% strand | P54132 |
| B, C, E | Bloom syndrome PROTEIN,BLOOM syndrome protein (EC 3.6.4.12) | protein | 513 | 50% helix, 12% strand | P54132 |
| D | Bloom syndrome PROTEIN,BLOOM syndrome protein (EC 3.6.4.12) | protein | 510 | 50% helix, 13% strand | P54132 |
| F | Bloom syndrome PROTEIN,BLOOM syndrome protein (EC 3.6.4.12) | protein | 516 | 49% helix, 12% strand | P54132 |
| M, N, O, P, Q, R | DNA (5'-D(*GP*TP*AP*CP*CP*CP*GP*AP*TP*GP*TP*GP*T)-3') | dna | 13 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- RY8 · N-(2,3-dimethyl-5-sulfamoylphenyl)-4-(2-methylthiazol-4-yl)benzamide · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains E, M, N, P, Q, A
- PG4 · Tetraethylene glycol · additive · 7 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.82 | 0.92 | 46 | RY8 |
| 2 | 1169 | 0.81 | 0.82 | 113 | ADP, RY8 |
| 3 | 977 | 0.81 | 0.82 | 102 | RY8, PG4 |
| 4 | 769 | 0.80 | 0.84 | 93 | RY8 |
| 5 | 900 | 0.78 | 0.80 | 83 | RY8 |
Interfaces
18 interfaces between chains.
- A–M · 1198 Ų buried · 28 hydrogen bonds · protein-nucleic
- E–Q · 1184 Ų buried · 27 hydrogen bonds · protein-nucleic
- D–P · 1160 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–O · 1154 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–N · 1151 Ų buried · 24 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7AUD · Structure of an engineered helicase domain construct for human Bloom syndrome protein… · the same entry in another collection · chain R against R, 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 P54132
- Elsewhere: RCSB PDB 7AUD · PDBe 7AUD · UniProt P54132
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