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The dodecamer structure of mcm from archaeal M. thermoautotrophicum
Analyse The dodecamer structure of mcm from archaeal M. thermoautotrophicum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LTL
- Type
- protein
- Length
- 1,437 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication initiator (CDC21/CDC54)
- UniProt
- O27798
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | DNA replication initiator (CDC21/CDC54) | protein | 239 | 26% helix, 35% strand | O27798 |
| E | DNA replication initiator (CDC21/CDC54) | protein | 242 | 28% helix, 33% strand | O27798 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.75 | 0.79 | 79 | empty |
| 2 | 579 | 0.74 | 0.82 | 68 | empty |
| 3 | 1140 | 0.73 | 0.77 | 95 | empty |
| 4 | 301 | 0.70 | 0.84 | 31 | empty |
| 5 | 325 | 0.69 | 0.83 | 31 | empty |
Interfaces
6 interfaces between chains.
- E–F · 842 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 792 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 791 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 191 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 184 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1LTL · The dodecamer structure of mcm from archaeal M. thermoautotrophicum · 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 O27798
- Elsewhere: RCSB PDB 1LTL · PDBe 1LTL · UniProt O27798
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