MolNFT v1 · #136939 · protein + DNA
Structural basis of MCM2-7 replicative helicase loading by orc-CDC6 and CDT1
5V8F · DNA replication licensing factor MCM2: “Structural basis of MCM2-7 replicative helicase loading by orc-CDC6 and CDT1”. Electron microscopy, 1 ligand (AGS), 20 pockets (best druggability 0.89). MolNFT v1 #136939 on GenesisL1: 3D…
- PDB
- 5V8F
- Type
- protein + DNA
- Length
- 7,297 residues
- Chains
- 16
- 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, P47112, P09119, P54784, P32833, P54790, P50874, P54791, P38826
- Ligands
- AGS
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 16 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 603 | 39% helix, 17% strand | P29469 |
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 654 | 37% helix, 15% strand | P24279 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 741 | 38% helix, 16% strand | P30665 |
| 5 | Minichromosome maintenance protein 5 (EC 3.6.4.12) | protein | 580 | 31% helix, 15% strand | P29496 |
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 692 | 37% helix, 16% strand | P53091 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 725 | 37% helix, 14% strand | P38132 |
| 8 | Cell division cycle protein CDT1 | protein | 519 | 36% helix, 8% strand | P47112 |
| 9 | Cell division control protein 6 | protein | 373 | 46% helix, 8% strand | P09119 |
| A | Origin recognition complex subunit 1 | protein | 425 | 50% helix, 9% strand | P54784 |
| B | Origin recognition complex subunit 2 | protein | 328 | 52% helix, 10% strand | P32833 |
| C | Origin recognition complex subunit 3 | protein | 544 | 53% helix, 8% strand | P54790 |
| E | Origin recognition complex subunit 5 | protein | 422 | 48% helix, 8% strand | P50874 |
| D | Origin recognition complex subunit 4 | protein | 456 | 54% helix, 8% strand | P54791 |
| F | Origin recognition complex subunit 6 | protein | 157 | 66% helix, 0% strand | P38826 |
| M | DNA (39-mer) | dna | 39 | — | — |
| N | DNA (39-mer) | dna | 39 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 8 copies · chains 2, 6, 4, 7, 3, 9, A, D, E
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 | 828 | 0.89 | 0.92 | 117 | empty |
| 2 | 1106 | 0.87 | 0.88 | 123 | empty |
| 3 | 368 | 0.86 | 0.94 | 47 | empty |
| 4 | 639 | 0.85 | 0.90 | 81 | empty |
| 5 | 994 | 0.85 | 0.86 | 94 | AGS |
Interfaces
60 interfaces between chains.
- 4–6 · 4402 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 4301 Ų buried · 50 hydrogen bonds · protein-protein
- A–D · 4291 Ų buried · 58 hydrogen bonds · protein-protein
- 4–7 · 4243 Ų buried · 45 hydrogen bonds · protein-protein
- 3–7 · 3709 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5V8F · Structural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1 · the same entry in another collection · chain B against B, 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
- Every structure of UniProt P47112
- Every structure of UniProt P09119
- Every structure of UniProt P54784
- Every structure of UniProt P32833
- Every structure of UniProt P54790
- Every structure of UniProt P50874
- Every structure of UniProt P54791
- Every structure of UniProt P38826
- Elsewhere: RCSB PDB 5V8F · PDBe 5V8F · UniProt P29469 · UniProt P24279 · UniProt P30665 · UniProt P29496 · UniProt P53091 · UniProt P38132 · UniProt P47112 · UniProt P09119 · UniProt P54784 · UniProt P32833 · UniProt P54790 · UniProt P50874 · UniProt P54791 · UniProt P38826
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