MolNFT v1 · #87975 · protein + DNA
Crystal structure of the BLOOM'S syndrome helicase blm in complex with DNA
4CGZ: “Crystal structure of the BLOOM'S syndrome helicase blm in complex with DNA”. X-ray diffraction, 2 ligands (ADP, ZN), 7 pockets (best druggability 0.84). MolNFT v1 #87975 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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