MolNFT v1 · #80681 · protein + DNA
Crystal structure of addab-DNA complex
3U44 · ATP-dependent HELICASE/NUCLEASE subunit a: “Crystal structure of addab-DNA complex”. X-ray diffraction, 1 ligand (SF4), 20 pockets (best druggability 0.83). MolNFT v1 #80681 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3U44
- Type
- protein + DNA
- Length
- 2,299 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 0.83
Structure
x-ray diffraction · 3 distinct chains · 51% 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 | 1122 | 53% helix, 14% strand | P23478 |
| B | ATP-dependent HELICASE/DEOXYRIBONUCLEASE subunit B (EC 3.1.-.-, 3.6.4.12) | protein | 1141 | 50% helix, 13% strand | P23477 |
| X | DNA (36-mer) | dna | 36 | — | — |
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 | 1087 | 0.83 | 0.84 | 103 | empty |
| 2 | 693 | 0.83 | 0.86 | 71 | empty |
| 3 | 319 | 0.82 | 0.92 | 42 | empty |
| 4 | 165 | 0.78 | 0.94 | 29 | empty |
| 5 | 537 | 0.78 | 0.85 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–B · 9766 Ų buried · 146 hydrogen bonds · protein-protein
- A–X · 881 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–X · 556 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 3U44 · Crystal structure of AddAB-DNA complex · 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 0.99
- 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 0.96
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 3U44 · PDBe 3U44 · UniProt P23478 · UniProt P23477
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