Research workbench
Structure of amppcp-bound dnaa from aquifex aeolicus
Analyse Structure of amppcp-bound dnaa from aquifex aeolicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HCB
- Type
- protein
- Length
- 1,272 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromosomal replication initiator protein dnaa
- UniProt
- O66659
- Ligands
- ACP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromosomal replication initiator protein dnaa | protein | 317 | 56% helix, 8% strand | O66659 |
| B | Chromosomal replication initiator protein dnaa | protein | 318 | 53% helix, 8% strand | O66659 |
| C | Chromosomal replication initiator protein dnaa | protein | 317 | 54% helix, 8% strand | O66659 |
| D | Chromosomal replication initiator protein dnaa | protein | 320 | 54% helix, 8% strand | O66659 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
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 | 953 | 0.83 | 0.84 | 100 | ACP |
| 2 | 1022 | 0.80 | 0.82 | 103 | ACP |
| 3 | 523 | 0.80 | 0.87 | 68 | MG, ACP |
| 4 | 562 | 0.78 | 0.84 | 62 | empty |
| 5 | 141 | 0.65 | 0.87 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1875 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1820 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1815 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2HCB · Structure of AMPPCP-bound DnaA from Aquifex aeolicus · the same entry in another collection · chain D against D, TM-score 1.00
- O66659 · AlphaFold monomer V2.0 prediction for chromosomal replication initiator protein dnaa… · a predicted model of the same protein · chain D against A, TM-score 0.85
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 O66659
- Elsewhere: RCSB PDB 2HCB · PDBe 2HCB · UniProt O66659
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