Research workbench
Crystal structure of addab with a forked DNA substrate
Analyse Crystal structure of addab with a forked DNA substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CEH
- Type
- protein + DNA
- Length
- 2,339 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent HELICASE/NUCLEASE subunit a; ATP-dependent HELICASE/DEOXYRIBONUCLEASE…
- EC
- 3.1.-.-, 3.6.4.12
- UniProt
- P23478, P23477
- Ligands
- SF4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent HELICASE/NUCLEASE subunit a (EC 3.1.-.-, 3.6.4.12) | protein | 1154 | 51% helix, 13% strand | P23478 |
| B | ATP-dependent HELICASE/DEOXYRIBONUCLEASE subunit B (EC 3.1.-.-, 3.6.4.12) | protein | 1148 | 49% helix, 13% strand | P23477 |
| X | DNA | dna | 37 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains B
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 | 850 | 0.86 | 0.89 | 104 | empty |
| 2 | 623 | 0.84 | 0.88 | 66 | empty |
| 3 | 941 | 0.83 | 0.85 | 109 | SF4 |
| 4 | 142 | 0.80 | 0.97 | 27 | empty |
| 5 | 826 | 0.79 | 0.82 | 65 | empty |
Interfaces
3 interfaces between chains.
- A–B · 9680 Ų buried · 119 hydrogen bonds · protein-protein
- A–X · 1698 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–X · 629 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 4CEH · Crystal structure of AddAB with a forked DNA substrate · the same entry in another collection · chain A against A, TM-score 1.00
- P23477 · AlphaFold monomer V2.0 prediction for ATP-dependent HELICASE/DEOXYRIBONUCLEASE subunit B… · a predicted model of the same protein · chain B against A, TM-score 1.00
- P23478 · AlphaFold monomer V2.0 prediction for ATP-dependent HELICASE/NUCLEASE subunit a (P23478) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P23478
- Every structure of UniProt P23477
- Elsewhere: RCSB PDB 4CEH · PDBe 4CEH · UniProt P23478 · UniProt P23477
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