Research workbench
Crystal structure of DUF1998 helicase mrfa bound to DNA and amppnp
Analyse Crystal structure of DUF1998 helicase mrfa bound to DNA and amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZNQ
- Type
- protein + DNA
- Length
- 1,487 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized ATP-dependent helicase ypra; Ssdna
- EC
- 3.6.4.-
- UniProt
- P50830
- Ligands
- ANP, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized ATP-dependent helicase ypra (EC 3.6.4.-) | protein | 748 | 37% helix, 25% strand | P50830 |
| B | Uncharacterized ATP-dependent helicase ypra (EC 3.6.4.-) | protein | 711 | 38% helix, 23% strand | P50830 |
| C, D | Ssdna | dna | 14 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.85 | 0.87 | 97 | empty |
| 2 | 661 | 0.84 | 0.88 | 64 | CIT |
| 3 | 778 | 0.75 | 0.80 | 69 | ANP |
| 4 | 749 | 0.74 | 0.80 | 66 | ANP |
| 5 | 315 | 0.68 | 0.83 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1183 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–D · 1170 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–D · 365 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- B–C · 60 Ų buried · 1 hydrogen bond · protein-nucleic
- A–D · 38 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 6ZNQ · Crystal Structure of DUF1998 helicase MrfA bound to DNA and AMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
- P50830 · AlphaFold monomer V2.0 prediction for uncharacterized ATP-dependent helicase ypra (P50830) · a predicted model of the same protein · chain B against A, TM-score 0.83
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 P50830
- Elsewhere: RCSB PDB 6ZNQ · PDBe 6ZNQ · UniProt P50830
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