MolNFT v1 · #148228 · protein + DNA
S. cerevisiae mcm double hexamer bound to duplex DNA
6F0L · DNA replication licensing factor MCM2: “S. cerevisiae mcm double hexamer bound to duplex DNA”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.90). MolNFT v1 #148228 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6F0L
- Type
- protein + DNA
- Length
- 7,678 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 0.90
Structure
electron microscopy · 8 distinct chains · 34% helix, 15% 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, 16% strand | P29469 |
| 3, B | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 596 | 35% helix, 15% strand | P24279 |
| 4, C | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 642 | 32% helix, 13% strand | P30665 |
| 5, D | Minichromosome maintenance protein 5 (EC 3.6.4.12) | protein | 634 | 36% helix, 16% strand | P29496 |
| 6, E | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 615 | 31% helix, 13% strand | P53091 |
| 7, F | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 687 | 33% helix, 17% strand | P38132 |
| X | DNA (62-mer) | dna | 62 | — | — |
| Y | DNA (62-mer) | dna | 62 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains 3, 5, 2, B, D, A
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 | 1172 | 0.90 | 0.91 | 163 | empty |
| 2 | 1158 | 0.89 | 0.91 | 188 | empty |
| 3 | 994 | 0.88 | 0.90 | 113 | ADP |
| 4 | 1021 | 0.87 | 0.89 | 118 | ADP |
| 5 | 951 | 0.87 | 0.89 | 115 | empty |
Interfaces
55 interfaces between chains.
- 4–7 · 4133 Ų buried · 40 hydrogen bonds · protein-protein
- C–F · 4130 Ų buried · 40 hydrogen bonds · protein-protein
- C–E · 4087 Ų buried · 25 hydrogen bonds · protein-protein
- 4–6 · 4078 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 3949 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6F0L · S. cerevisiae MCM double hexamer bound to duplex DNA · the same entry in another collection · chain Y against Y, 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 6F0L · PDBe 6F0L · UniProt P29469 · UniProt P24279 · UniProt P30665 · UniProt P29496 · UniProt P53091 · UniProt P38132
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