MolNFT v1 · #161439 · protein
E. COLI dnabc apo complex
6QEL · Replicative DNA helicase: “E. COLI dnabc apo complex”. Electron microscopy, 3 ligands (ADP, 08T, MG), 20 pockets (best druggability 0.87). MolNFT v1 #161439 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6QEL
- Type
- protein
- Length
- 4,092 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicative DNA helicase; DNA replication protein dnac
- EC
- 3.6.4.12
- UniProt
- E3PC72, L3QJA3
- Ligands
- ADP, 08T, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Replicative DNA helicase (EC 3.6.4.12) | protein | 450 | 50% helix, 10% strand | E3PC72 |
| B, D, F | Replicative DNA helicase (EC 3.6.4.12) | protein | 445 | 47% helix, 9% strand | E3PC72 |
| E | Replicative DNA helicase (EC 3.6.4.12) | protein | 443 | 50% helix, 9% strand | E3PC72 |
| G | DNA replication protein dnac | protein | 229 | 50% helix, 9% strand | L3QJA3 |
| H, I, J, K, L | DNA replication protein dnac | protein | 237 | 50% helix, 5% strand | L3QJA3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 7 copies · chains A, B, C, D, E, F, G
- 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 G, H, I, J, K, L
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 1128 | 0.87 | 0.88 | 115 | empty |
| 2 | 544 | 0.85 | 0.91 | 92 | empty |
| 3 | 392 | 0.82 | 0.90 | 50 | empty |
| 4 | 431 | 0.81 | 0.89 | 56 | empty |
| 5 | 1013 | 0.80 | 0.82 | 98 | 08T, MG |
Interfaces
25 interfaces between chains.
- B–C · 3297 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 3289 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3202 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 3185 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 3169 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6QEL · E. coli DnaBC apo complex · the same entry in another collection · chain A against A, 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 E3PC72
- Every structure of UniProt L3QJA3
- Elsewhere: RCSB PDB 6QEL · PDBe 6QEL · UniProt E3PC72 · UniProt L3QJA3
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