Research workbench
Atomic model of semi-attached mutant occm-DNA complex (orc-CDC6-CDT1- MCM2-7 with MCM6 whd truncation)
Analyse Atomic model of semi-attached mutant occm-DNA complex (orc-CDC6-CDT1- MCM2-7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WGC
- Type
- protein + DNA
- Length
- 2,886 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 6; Origin recognition complex subunit 1; Origin recognition…
- EC
- 3.6.4.12
- UniProt
- P09119, P54784, P32833, P54790, P50874, P54791, P38826, P24279, P38132
- Ligands
- AGS
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 11 distinct chains · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 9 | Cell division control protein 6 | protein | 373 | 39% helix, 7% strand | P09119 |
| A | Origin recognition complex subunit 1 | protein | 425 | 46% helix, 11% strand | P54784 |
| B | Origin recognition complex subunit 2 | protein | 326 | 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 | 43% helix, 8% strand | P50874 |
| D | Origin recognition complex subunit 4 | protein | 436 | 53% helix, 8% strand | P54791 |
| F | Origin recognition complex subunit 6 | protein | 157 | 63% helix, 0% strand | P38826 |
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 69 | 42% helix, 6% strand | P24279 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 52 | 54% helix, 0% strand | P38132 |
| G | DNA (41-mer) | dna | 41 | — | — |
| H | DNA (41-mer) | dna | 41 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains 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 | 928 | 0.88 | 0.90 | 124 | empty |
| 2 | 647 | 0.87 | 0.92 | 76 | empty |
| 3 | 671 | 0.86 | 0.90 | 97 | AGS |
| 4 | 796 | 0.84 | 0.87 | 96 | empty |
| 5 | 1131 | 0.84 | 0.84 | 89 | AGS |
Interfaces
30 interfaces between chains.
- A–D · 4526 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 4247 Ų buried · 38 hydrogen bonds · protein-protein
- E–D · 2975 Ų buried · 29 hydrogen bonds · protein-protein
- C–E · 2374 Ų buried · 13 hydrogen bonds · protein-protein
- 9–A · 2096 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6WGC · Atomic model of semi-attached mutant OCCM-DNA complex (ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD… · the same entry in another collection · chain H against H, TM-score 1.00
- P54791 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 4 (P54791) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 P24279
- Every structure of UniProt P38132
- Elsewhere: RCSB PDB 6WGC · PDBe 6WGC · UniProt P09119 · UniProt P54784 · UniProt P32833 · UniProt P54790 · UniProt P50874 · UniProt P54791 · UniProt P38826 · UniProt P24279 · UniProt P38132
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