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Ternary complex of BLOOM'S syndrome helicase
Analyse Ternary complex of BLOOM'S syndrome helicase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O3M
- Type
- protein + DNA
- Length
- 641 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bloom syndrome protein; 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*AP*AP*G)-3'…
- EC
- 3.6.4.12
- UniProt
- P54132
- Ligands
- ADP, CA, ZN
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bloom syndrome protein (EC 3.6.4.12) | protein | 613 | 46% helix, 13% strand | P54132 |
| P | 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*AP*AP*G)-3' | dna | 12 | — | — |
| T | 5'-D(*CP*TP*TP*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP *CP*CP*CP*TP*TP*A)-3' | dna | 16 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- CA · Calcium ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.84 | 0.85 | 73 | CA, ADP, EDO |
| 2 | 875 | 0.73 | 0.78 | 53 | empty |
| 3 | 266 | 0.65 | 0.82 | 29 | empty |
| 4 | 179 | 0.60 | 0.83 | 33 | empty |
| 5 | 61 | 0.49 | 0.85 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–T · 918 Ų buried · 21 hydrogen bonds · protein-nucleic
- P–T · 520 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- A–P · 507 Ų buried · 6 hydrogen bonds · protein-nucleic
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 4O3M · PDBe 4O3M · UniProt P54132
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