MolNFT v1 · #114321 · protein + DNA
Cryo-EM structure of MCM2-7 double hexamer on dsdna
5BK4 · DNA replication licensing factor MCM2: “Cryo-EM structure of MCM2-7 double hexamer on dsdna”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.87). MolNFT v1 #114321 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5BK4
- Type
- protein + DNA
- Length
- 7,756 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication licensing factor MCM2; DNA replication licensing factor MCM3; DNA…
- EC
- 3.6.4.12
- UniProt
- P29469, P24279, P30665, P29496, P53091, P38132
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 8 distinct chains · 32% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2, A | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 603 | 34% helix, 15% strand | P29469 |
| 3, B | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 604 | 34% helix, 15% strand | P24279 |
| 4, C | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 646 | 31% helix, 13% strand | P30665 |
| 5, D | DNA replication licensing factor MCM5 (EC 3.6.4.12) | protein | 661 | 31% helix, 15% strand | P29496 |
| 6, E | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 615 | 30% helix, 13% strand | P53091 |
| 7, F | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 689 | 33% helix, 13% strand | P38132 |
| S | DNA (60-mer), strand 1 | dna | 60 | — | — |
| O | DNA (60-mer), strand 2 | dna | 60 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains 2, 6, 3, 5, 7, A, E, B, D, F
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 | 892 | 0.87 | 0.89 | 92 | empty |
| 2 | 950 | 0.87 | 0.89 | 99 | ADP |
| 3 | 877 | 0.87 | 0.89 | 84 | ADP |
| 4 | 880 | 0.86 | 0.88 | 109 | empty |
| 5 | 684 | 0.86 | 0.90 | 83 | empty |
Interfaces
53 interfaces between chains.
- 4–7 · 4191 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 4141 Ų buried · 23 hydrogen bonds · protein-protein
- 4–6 · 4098 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 4091 Ų buried · 21 hydrogen bonds · protein-protein
- 3–5 · 3874 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5BK4 · Cryo-EM structure of Mcm2-7 double hexamer on dsDNA · the same entry in another collection · chain O against O, 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 P29469
- Every structure of UniProt P24279
- Every structure of UniProt P30665
- Every structure of UniProt P29496
- Every structure of UniProt P53091
- Every structure of UniProt P38132
- Elsewhere: RCSB PDB 5BK4 · PDBe 5BK4 · UniProt P29469 · UniProt P24279 · UniProt P30665 · UniProt P29496 · UniProt P53091 · UniProt P38132
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