Research workbench
Cryo-EM structure of the fork protection complex bound to cmg at a replication fork - conformation 2 mcm CTD:SSDNA
Analyse Cryo-EM structure of the fork protection complex bound to cmg at a replication… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SKO
- Type
- protein + DNA
- Length
- 1,971 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication licensing factor MCM6; DNA replication licensing factor MCM7; DNA…
- EC
- 3.6.4.12
- UniProt
- P53091, P38132, P29469, P29496, P24279, P30665
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 7 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 328 | 44% helix, 15% strand | P53091 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 335 | 47% helix, 16% strand | P38132 |
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 346 | 49% helix, 14% strand | P29469 |
| 5 | Minichromosome maintenance protein 5 (EC 3.6.4.12) | protein | 280 | 47% helix, 18% strand | P29496 |
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 336 | 43% helix, 16% strand | P24279 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 330 | 45% helix, 17% strand | P30665 |
| I | Ssdna, leading-strand template | dna | 16 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 5 copies · chains 6, 4, 7, 3, 2, 5
- MG · Magnesium ion · metal · 5 copies · chains 6, 4, 7, 3, 2, 5
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.84 | 0.85 | 124 | ANP, MG |
| 2 | 616 | 0.82 | 0.87 | 80 | ANP, MG |
| 3 | 602 | 0.80 | 0.86 | 71 | ANP, MG |
| 4 | 491 | 0.80 | 0.87 | 64 | ANP, MG |
| 5 | 1046 | 0.79 | 0.80 | 124 | ANP |
Interfaces
12 interfaces between chains.
- 7–4 · 2443 Ų buried · 29 hydrogen bonds · protein-protein
- 5–3 · 2307 Ų buried · 24 hydrogen bonds · protein-protein
- 7–3 · 2234 Ų buried · 25 hydrogen bonds · protein-protein
- 6–2 · 2187 Ų buried · 21 hydrogen bonds · protein-protein
- 6–4 · 2021 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6SKO · Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork… · the same entry in another collection · chain I against I, TM-score 1.00
- P53091 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM6 (P53091) · a predicted model of the same protein · chain 6 against A, TM-score 0.98
- P38132 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM7 (P38132) · a predicted model of the same protein · chain 7 against A, TM-score 0.97
- P24279 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM3 (P24279) · a predicted model of the same protein · chain 3 against A, TM-score 0.97
- P29469 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM2 (P29469) · a predicted model of the same protein · chain 2 against A, TM-score 0.95
- P30665 · AlphaFold monomer V2.0 prediction for DNA replication licensing factor MCM4 (P30665) · a predicted model of the same protein · chain 4 against A, TM-score 0.93
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 P53091
- Every structure of UniProt P38132
- Every structure of UniProt P29469
- Every structure of UniProt P29496
- Every structure of UniProt P24279
- Every structure of UniProt P30665
- Elsewhere: RCSB PDB 6SKO · PDBe 6SKO · UniProt P53091 · UniProt P38132 · UniProt P29469 · UniProt P29496 · UniProt P24279 · UniProt P30665
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