Research workbench
Crystal structure of the BLOOM'S syndrome helicase blm in complex with nanobody
Analyse Crystal structure of the BLOOM'S syndrome helicase blm in complex with nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CDG
- Type
- protein
- Length
- 1,485 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bloom syndrome protein; Nanobody
- EC
- 3.6.4.12
- UniProt
- P54132
- Ligands
- ADP, ZN
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bloom syndrome protein (EC 3.6.4.12) | protein | 625 | 46% helix, 13% strand | P54132 |
| B | Bloom syndrome protein (EC 3.6.4.12) | protein | 616 | 47% helix, 14% strand | P54132 |
| C, D | Nanobody | protein | 122 | 5% helix, 52% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.84 | 0.88 | 73 | ADP |
| 2 | 806 | 0.83 | 0.85 | 84 | ADP |
| 3 | 624 | 0.67 | 0.76 | 56 | empty |
| 4 | 674 | 0.63 | 0.74 | 68 | empty |
| 5 | 574 | 0.60 | 0.73 | 54 | empty |
Interfaces
3 interfaces between chains.
- B–D · 903 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 890 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 587 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4CDG · Crystal structure of the Bloom's syndrome helicase BLM in complex with Nanobody · 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 0.78
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 4CDG · PDBe 4CDG · UniProt P54132
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.