Research workbench
Crystal structure of domain III from the thermotoga maritima replication initiation protein dnaa
Analyse Crystal structure of domain III from the thermotoga maritima replication… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z4R
- Type
- protein
- Length
- 720 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromosomal replication initiator protein dnaa
- UniProt
- P46798
- Ligands
- ADP, MG
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Chromosomal replication initiator protein dnaa | protein | 240 | 54% helix, 10% strand | P46798 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.73 | 0.88 | 32 | ADP, MG |
| 2 | 208 | 0.70 | 0.87 | 31 | ADP, MG |
| 3 | 199 | 0.70 | 0.87 | 27 | ADP, MG |
| 4 | 172 | 0.49 | 0.77 | 20 | empty |
| 5 | 104 | 0.43 | 0.78 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–C · 705 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 617 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2Z4R · Crystal structure of domain III from the Thermotoga maritima replication initiation… · the same entry in another collection · chain A against A, TM-score 1.00
- P46798 · AlphaFold monomer V2.0 prediction for chromosomal replication initiator protein dnaa… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P46798
- Elsewhere: RCSB PDB 2Z4R · PDBe 2Z4R · UniProt P46798
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