Research workbench
Mechanisms of opening and closing of the bacterial replicative helicase: the dnab helicase and lambda P helicase loader complex
Analyse Mechanisms of opening and closing of the bacterial replicative helicase: the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BBM
- Type
- protein
- Length
- 3,280 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicative DNA helicase; Replication protein P
- EC
- 3.6.4.12
- UniProt
- A0A365Q7M1, P03689
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 10 distinct chains · 35% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicative DNA helicase (EC 3.6.4.12) | protein | 405 | 35% helix, 12% strand | A0A365Q7M1 |
| B | Replicative DNA helicase (EC 3.6.4.12) | protein | 447 | 36% helix, 9% strand | A0A365Q7M1 |
| C | Replicative DNA helicase (EC 3.6.4.12) | protein | 453 | 34% helix, 9% strand | A0A365Q7M1 |
| D | Replicative DNA helicase (EC 3.6.4.12) | protein | 455 | 35% helix, 8% strand | A0A365Q7M1 |
| E | Replicative DNA helicase (EC 3.6.4.12) | protein | 454 | 36% helix, 8% strand | A0A365Q7M1 |
| F | Replicative DNA helicase (EC 3.6.4.12) | protein | 448 | 39% helix, 8% strand | A0A365Q7M1 |
| V, W | Replication protein P | protein | 125 | 34% helix, 0% strand | P03689 |
| X | Replication protein P | protein | 121 | 32% helix, 0% strand | P03689 |
| Y | Replication protein P | protein | 124 | 31% helix, 0% strand | P03689 |
| Z | Replication protein P | protein | 123 | 37% helix, 2% strand | P03689 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, F, B, C, D, E, W
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 | 1021 | 0.87 | 0.88 | 88 | empty |
| 2 | 984 | 0.84 | 0.86 | 110 | ADP |
| 3 | 1044 | 0.84 | 0.86 | 120 | ADP |
| 4 | 505 | 0.84 | 0.91 | 39 | empty |
| 5 | 1066 | 0.84 | 0.85 | 102 | ADP |
Interfaces
21 interfaces between chains.
- B–C · 3606 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 3587 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 3554 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 3383 Ų buried · 39 hydrogen bonds · protein-protein
- A–F · 3160 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6BBM · Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB… · 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 A0A365Q7M1
- Every structure of UniProt P03689
- Elsewhere: RCSB PDB 6BBM · PDBe 6BBM · UniProt A0A365Q7M1 · UniProt P03689
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