Research workbench
Cryo-EM structure of adna-ADNB(W325A) in complex with DNA and amppnp
Analyse Cryo-EM structure of adna-ADNB(W325A) in complex with 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
- 7SJR
- Type
- protein + DNA
- Length
- 1,748 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA helicase; DNA (70-mer)
- EC
- 3.6.4.12
- UniProt
- A0A653FJ17, A0A0D6HKQ2
- Ligands
- SF4, ANP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA helicase (EC 3.6.4.12) | protein | 802 | 45% helix, 6% strand | A0A653FJ17 |
| A | DNA helicase (EC 3.6.4.12) | protein | 911 | 47% helix, 8% strand | A0A0D6HKQ2 |
| C | DNA (70-mer) | dna | 35 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.82 | 0.84 | 128 | empty |
| 2 | 944 | 0.79 | 0.81 | 78 | empty |
| 3 | 1105 | 0.75 | 0.77 | 113 | ANP |
| 4 | 477 | 0.73 | 0.82 | 59 | empty |
| 5 | 500 | 0.72 | 0.82 | 44 | empty |
Interfaces
3 interfaces between chains.
- B–A · 6494 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 1450 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 643 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 7SJR · Cryo-EM structure of AdnA-AdnB(W325A) in complex with DNA and 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 A0A653FJ17
- Every structure of UniProt A0A0D6HKQ2
- Elsewhere: RCSB PDB 7SJR · PDBe 7SJR · UniProt A0A653FJ17 · UniProt A0A0D6HKQ2
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