MolNFT v1 · #160621 · protein + DNA
Cryo-EM structure of ADNA(D934A)-ADNB(D1014A) in complex with amppnp and DNA
6PPR · UVRD/REP helicase: “Cryo-EM structure of ADNA(D934A)-ADNB(D1014A) in complex with amppnp and DNA”. Electron microscopy, 2 ligands (ANP, SF4), 20 pockets (best druggability 0.84). MolNFT v1 #160621 on GenesisL1: 3D structure, binding…
- PDB
- 6PPR
- Type
- protein + DNA
- Length
- 1,626 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UVRD/REP helicase; ATP-dependent DNA helicase (UVRD/REP); DNA (70-mer)
- EC
- 3.6.4.12
- UniProt
- A0A0D6HIW1, A0A0D6HKQ2
- Ligands
- ANP, SF4
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 37% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | UVRD/REP helicase (EC 3.6.4.12) | protein | 760 | 34% helix, 6% strand | A0A0D6HIW1 |
| A | ATP-dependent DNA helicase (UVRD/REP) (EC 3.6.4.12) | protein | 834 | 39% helix, 9% strand | A0A0D6HKQ2 |
| X | DNA (70-mer) | dna | 32 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- SF4 · Iron/sulfur cluster · ligand · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.84 | 0.85 | 122 | empty |
| 2 | 1101 | 0.77 | 0.79 | 97 | empty |
| 3 | 661 | 0.76 | 0.82 | 81 | SF4 |
| 4 | 504 | 0.71 | 0.81 | 69 | empty |
| 5 | 456 | 0.66 | 0.78 | 49 | ANP |
Interfaces
3 interfaces between chains.
- B–A · 5482 Ų buried · 31 hydrogen bonds · protein-protein
- B–X · 1336 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–X · 921 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 6PPR · Cryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and DNA · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A0D6HIW1
- Every structure of UniProt A0A0D6HKQ2
- Elsewhere: RCSB PDB 6PPR · PDBe 6PPR · UniProt A0A0D6HIW1 · UniProt A0A0D6HKQ2
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