Research workbench
Crystal structure of xenopus laevis replication initiation factor MCM10 internal domain
Analyse Crystal structure of xenopus laevis replication initiation factor MCM10… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EBE
- Type
- protein
- Length
- 515 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein MCM10 homolog
- UniProt
- Q5EAW4
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein MCM10 homolog | protein | 172 | 20% helix, 32% strand | Q5EAW4 |
| B | Protein MCM10 homolog | protein | 166 | 16% helix, 36% strand | Q5EAW4 |
| C | Protein MCM10 homolog | protein | 177 | 21% helix, 32% strand | Q5EAW4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.72 | 0.79 | 78 | empty |
| 2 | 206 | 0.60 | 0.82 | 34 | empty |
| 3 | 60 | 0.34 | 0.77 | 20 | empty |
| 4 | 61 | 0.33 | 0.77 | 15 | empty |
| 5 | 69 | 0.32 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1080 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 657 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3EBE · Crystal structure of xenopus laevis replication initiation factor MCM10 internal domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q5EAW4 · AlphaFold monomer V2.0 prediction for protein MCM10 homolog (Q5EAW4) · a predicted model of the same protein · chain A 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 Q5EAW4
- Elsewhere: RCSB PDB 3EBE · PDBe 3EBE · UniProt Q5EAW4
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