MolNFT v1 · #161440 · protein + DNA
E. COLI dnabc complex bound to ssdna
6QEM · Replicative DNA helicase: “E. COLI dnabc complex bound to ssdna”. Electron microscopy, 3 ligands (ADP, 08T, MG), 20 pockets (best druggability 0.79). MolNFT v1 #161440 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6QEM
- Type
- protein + DNA
- Length
- 4,130 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicative DNA helicase; DNA replication protein dnac; Ssdna
- EC
- 3.6.4.12
- UniProt
- P0ACB0, P0AEF0
- Ligands
- ADP, 08T, MG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Replicative DNA helicase (EC 3.6.4.12) | protein | 445 | 48% helix, 10% strand | P0ACB0 |
| G, H, I, J, K, L | DNA replication protein dnac (EC 3.6.4.12) | protein | 239 | 53% helix, 8% strand | P0AEF0 |
| M | Ssdna | dna | 26 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains G, L, H, I, J, K
- 08T · [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium · ligand · 5 copies · chains A, F, B, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
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 | 504 | 0.79 | 0.86 | 78 | 08T, MG |
| 2 | 945 | 0.79 | 0.81 | 91 | empty |
| 3 | 893 | 0.79 | 0.81 | 86 | empty |
| 4 | 149 | 0.78 | 0.95 | 29 | empty |
| 5 | 475 | 0.76 | 0.85 | 74 | 08T, MG |
Interfaces
38 interfaces between chains.
- C–D · 3406 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 3334 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 2688 Ų buried · 43 hydrogen bonds · protein-protein
- A–F · 2655 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 2339 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6QEM · E. coli DnaBC complex bound to ssDNA · the same entry in another collection · chain K against K, 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 P0ACB0
- Every structure of UniProt P0AEF0
- Elsewhere: RCSB PDB 6QEM · PDBe 6QEM · UniProt P0ACB0 · UniProt P0AEF0
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