Research workbench
Atomic model of mutant MCM2-7 hexamer with MCM6 whd truncation
Analyse Atomic model of mutant MCM2-7 hexamer with MCM6 whd truncation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WGF
- Type
- protein
- Length
- 3,435 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication licensing factor MCM2; DNA replication licensing factor MCM7; DNA…
- EC
- 3.6.4.12
- UniProt
- P29469, P38132, P53091, P29496, P30665, P24279
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 6 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 508 | 33% helix, 21% strand | P29469 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 563 | 33% helix, 21% strand | P38132 |
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 564 | 34% helix, 18% strand | P53091 |
| 5 | Minichromosome maintenance protein 5 (EC 3.6.4.12) | protein | 598 | 41% helix, 18% strand | P29496 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 636 | 36% helix, 18% strand | P30665 |
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 566 | 32% helix, 18% strand | P24279 |
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 | 1142 | 0.87 | 0.88 | 109 | empty |
| 2 | 1029 | 0.85 | 0.86 | 118 | empty |
| 3 | 764 | 0.85 | 0.89 | 97 | empty |
| 4 | 1071 | 0.84 | 0.85 | 115 | empty |
| 5 | 948 | 0.84 | 0.85 | 129 | empty |
Interfaces
8 interfaces between chains.
- 5–3 · 2254 Ų buried · 15 hydrogen bonds · protein-protein
- 2–6 · 2083 Ų buried · 13 hydrogen bonds · protein-protein
- 6–4 · 2035 Ų buried · 14 hydrogen bonds · protein-protein
- 7–3 · 1682 Ų buried · 9 hydrogen bonds · protein-protein
- 7–4 · 1659 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6WGF · Atomic model of mutant Mcm2-7 hexamer with Mcm6 WHD truncation · the same entry in another collection · chain 3 against 3, TM-score 1.00
- 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 0.77
- P29496 · AlphaFold monomer V2.0 prediction for minichromosome maintenance protein 5 (P29496) · a predicted model of the same protein · chain 5 against A, TM-score 0.75
- 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 0.74
- 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 0.71
- 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 0.64
- 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 0.59
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 P38132
- Every structure of UniProt P53091
- Every structure of UniProt P29496
- Every structure of UniProt P30665
- Every structure of UniProt P24279
- Elsewhere: RCSB PDB 6WGF · PDBe 6WGF · UniProt P29469 · UniProt P38132 · UniProt P53091 · UniProt P29496 · UniProt P30665 · UniProt P24279
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