MolNFT v1 · #87890 · protein + DNA
Crystal structure of addab-DNA-adpnp complex at 3 ångström resolution
4CEJ · ATP-dependent HELICASE/NUCLEASE subunit a: “Crystal structure of addab-DNA-adpnp complex at 3 ångström resolution”. X-ray diffraction, 3 ligands (ANP, SF4, MG), 20 pockets (best druggability 0.84). MolNFT v1 #87890 on GenesisL1: 3D…
- PDB
- 4CEJ
- Type
- protein + DNA
- Length
- 2,378 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
- ANP, SF4, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 52% 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 | 1177 | 53% helix, 13% strand | P23478 |
| B | ATP-dependent HELICASE/DEOXYRIBONUCLEASE subunit B (EC 3.1.-.-, 3.6.4.12) | protein | 1156 | 51% helix, 13% strand | P23477 |
| X | DNA | dna | 45 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, 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 | 651 | 0.84 | 0.88 | 68 | empty |
| 2 | 465 | 0.84 | 0.91 | 58 | empty |
| 3 | 423 | 0.83 | 0.91 | 50 | empty |
| 4 | 730 | 0.83 | 0.86 | 77 | empty |
| 5 | 375 | 0.83 | 0.92 | 69 | empty |
Interfaces
3 interfaces between chains.
- A–B · 10234 Ų buried · 124 hydrogen bonds · protein-protein
- A–X · 2074 Ų buried · 35 hydrogen bonds · protein-nucleic
- B–X · 1649 Ų buried · 32 hydrogen bonds · protein-nucleic
Compared structures
- 4CEJ · Crystal structure of AddAB-DNA-ADPNP complex at 3 Angstrom resolution · 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 0.98
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 4CEJ · PDBe 4CEJ · UniProt P23478 · UniProt P23477
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