Research workbench
Crystal structure of the BLOOM'S syndrome helicase blm in complex with DNA
Analyse Crystal structure of the BLOOM'S syndrome helicase blm in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CGZ
- Type
- protein + DNA
- Length
- 658 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BLOOM'S syndrome helicase; 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP)-3'…
- EC
- 3.6.4.12
- UniProt
- P54132
- Ligands
- ADP, ZN
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BLOOM'S syndrome helicase (EC 3.6.4.12) | protein | 629 | 46% helix, 12% strand | P54132 |
| B | 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP)-3' | dna | 12 | — | — |
| C | 5'-D(*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*DT *CP*CP*CP)-3' | dna | 17 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.84 | 0.85 | 107 | ADP |
| 2 | 1132 | 0.76 | 0.79 | 73 | empty |
| 3 | 354 | 0.72 | 0.84 | 33 | empty |
| 4 | 194 | 0.49 | 0.76 | 25 | empty |
| 5 | 83 | 0.40 | 0.78 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1016 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 536 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- A–B · 430 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4CGZ · Crystal structure of the Bloom's syndrome helicase BLM in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P54132 · AlphaFold monomer V2.0 prediction for bloom syndrome protein (P54132) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 4CGZ · PDBe 4CGZ · UniProt P54132
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