MolNFT v1 · #160613 · protein
Cryo-EM structure of ADNA(D934A)-ADNB(D1014A) in complex with amppnp
6PPJ · UVRD/REP helicase: “Cryo-EM structure of ADNA(D934A)-ADNB(D1014A) in complex with amppnp”. Electron microscopy, 2 ligands (SF4, ANP), 20 pockets (best druggability 0.76). MolNFT v1 #160613 on GenesisL1: 3D structure, binding sites…
- PDB
- 6PPJ
- Type
- protein
- Length
- 1,749 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UVRD/REP helicase; ATP-dependent DNA helicase (UVRD/REP)
- EC
- 3.6.4.12
- UniProt
- A0A0D6HIW1, A0A0D6HKQ2
- Ligands
- SF4, ANP
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 2 distinct chains · 40% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | UVRD/REP helicase (EC 3.6.4.12) | protein | 848 | 42% helix, 9% strand | A0A0D6HIW1 |
| A | ATP-dependent DNA helicase (UVRD/REP) (EC 3.6.4.12) | protein | 901 | 39% helix, 9% strand | A0A0D6HKQ2 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.76 | 0.79 | 109 | empty |
| 2 | 1038 | 0.75 | 0.77 | 95 | empty |
| 3 | 583 | 0.71 | 0.79 | 55 | empty |
| 4 | 384 | 0.70 | 0.82 | 47 | ANP |
| 5 | 470 | 0.69 | 0.80 | 48 | empty |
Interfaces
1 interface between chains.
- B–A · 6793 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 6PPJ · Cryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP · 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 6PPJ · PDBe 6PPJ · UniProt A0A0D6HIW1 · UniProt A0A0D6HKQ2
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