MolNFT v1 · #168431 · protein + DNA
Atomic model of the mutant occm (orc-CDC6-CDT1-MCM2-7 with MCM6 whd truncation) loaded on DNA at 10.5 a resolution
6WGI · DNA (34-mer): “Atomic model of the mutant occm (orc-CDC6-CDT1-MCM2-7 with MCM6 whd truncation) loaded on DNA at 10.5 a…”. Electron microscopy, 2 ligands (AGS, MG), 20 pockets (best druggability 0.88). MolNFT v1 #168431 on GenesisL1…
- PDB
- 6WGI
- Type
- protein + DNA
- Length
- 6,689 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (34-mer); Cell division control protein 6; Origin recognition complex subunit 1…
- EC
- 3.6.4.12
- UniProt
- P09119, P54784, P32833, P54790, P50874, P54791, P38826, P29469, P24279, P30665, P29496, P47112, P53091, P38132
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 16 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | DNA (34-mer) | dna | 34 | — | — |
| H | DNA (34-mer) | dna | 34 | — | — |
| 9 | Cell division control protein 6 | protein | 373 | 39% helix, 7% strand | P09119 |
| A | Origin recognition complex subunit 1 | protein | 420 | 46% helix, 11% strand | P54784 |
| B | Origin recognition complex subunit 2 | protein | 325 | 48% helix, 10% strand | P32833 |
| C | Origin recognition complex subunit 3 | protein | 544 | 51% helix, 7% strand | P54790 |
| E | Origin recognition complex subunit 5 | protein | 422 | 42% helix, 8% strand | P50874 |
| D | Origin recognition complex subunit 4 | protein | 436 | 52% helix, 8% strand | P54791 |
| F | Origin recognition complex subunit 6 | protein | 157 | 63% helix, 0% strand | P38826 |
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 573 | 36% helix, 19% strand | P29469 |
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 637 | 35% helix, 19% strand | P24279 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 650 | 34% helix, 20% strand | P30665 |
| 5 | Minichromosome maintenance protein 5 (EC 3.6.4.12) | protein | 529 | 35% helix, 23% strand | P29496 |
| L | Cell division cycle protein CDT1 | protein | 367 | 30% helix, 9% strand | P47112 |
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 563 | 34% helix, 18% strand | P53091 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 625 | 35% helix, 19% strand | P38132 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains 9, A, D, E
- MG · Magnesium ion · metal · 2 copies · chains A, 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 | 718 | 0.88 | 0.91 | 90 | empty |
| 2 | 712 | 0.86 | 0.90 | 114 | empty |
| 3 | 1149 | 0.86 | 0.87 | 146 | AGS |
| 4 | 1092 | 0.86 | 0.87 | 119 | empty |
| 5 | 1001 | 0.85 | 0.86 | 143 | empty |
Interfaces
50 interfaces between chains.
- A–D · 4425 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 4208 Ų buried · 37 hydrogen bonds · protein-protein
- E–D · 2981 Ų buried · 29 hydrogen bonds · protein-protein
- 4–6 · 2486 Ų buried · 9 hydrogen bonds · protein-protein
- 3–7 · 2474 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6WGI · Atomic model of the mutant OCCM (ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD truncation) loaded on… · the same entry in another collection · chain 3 against 3, 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 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
- Every structure of UniProt P29469
- Every structure of UniProt P24279
- Every structure of UniProt P30665
- Every structure of UniProt P29496
- Every structure of UniProt P47112
- Every structure of UniProt P53091
- Every structure of UniProt P38132
- Elsewhere: RCSB PDB 6WGI · PDBe 6WGI · UniProt P09119 · UniProt P54784 · UniProt P32833 · UniProt P54790 · UniProt P50874 · UniProt P54791 · UniProt P38826 · UniProt P29469 · UniProt P24279 · UniProt P30665 · UniProt P29496 · UniProt P47112 · UniProt P53091 · UniProt P38132
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