Research workbench
Mcm-ssdna co-crystal structure
Analyse Mcm-ssdna co-crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4POG
- Type
- protein + DNA
- Length
- 3,083 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 21; 30-mer OLIGO(DT)
- UniProt
- Q8U3I4
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H, I, J, K, L | Cell division control protein 21 | protein | 255 | 24% helix, 32% strand | Q8U3I4 |
| G | Cell division control protein 21 | protein | 249 | 16% helix, 31% strand | Q8U3I4 |
| X, Z | 30-mer OLIGO(DT) | dna | 7 | — | — |
| V | 30-mer OLIGO(DT) | dna | 4 | — | — |
| Y | 30-mer OLIGO(DT) | dna | 11 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 1080 | 0.79 | 0.80 | 72 | empty |
| 2 | 1003 | 0.78 | 0.80 | 81 | empty |
| 3 | 1036 | 0.78 | 0.80 | 72 | empty |
| 4 | 955 | 0.75 | 0.78 | 62 | empty |
| 5 | 903 | 0.74 | 0.78 | 62 | empty |
Interfaces
30 interfaces between chains.
- I–J · 1064 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1063 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1041 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1040 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 987 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4POG · MCM-ssDNA co-crystal structure · 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 Q8U3I4
- Elsewhere: RCSB PDB 4POG · PDBe 4POG · UniProt Q8U3I4
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