Research workbench
Structure of the S. cerevisiae origin recognition complex bound to the replication initiator CDC6 and the ARS1 origin DNA.
Analyse Structure of the S. cerevisiae origin recognition complex bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MCA
- Type
- protein + DNA
- Length
- 2,860 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Origin recognition complex subunit 1; Origin recognition complex subunit 2; Origin…
- UniProt
- P54784, P32833, P54790, P54791, P50874, P38826, P09119
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 9 distinct chains · 41% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Origin recognition complex subunit 1 | protein | 493 | 41% helix, 9% strand | P54784 |
| B | Origin recognition complex subunit 2 | protein | 253 | 42% helix, 9% strand | P32833 |
| C | Origin recognition complex subunit 3 | protein | 584 | 45% helix, 8% strand | P54790 |
| D | Origin recognition complex subunit 4 | protein | 438 | 46% helix, 9% strand | P54791 |
| E | Origin recognition complex subunit 5 | protein | 452 | 36% helix, 7% strand | P50874 |
| F | Origin recognition complex subunit 6 | protein | 164 | 51% helix, 0% strand | P38826 |
| G | DNA (85-mer) | dna | 50 | — | — |
| H | DNA (85-mer) | dna | 50 | — | — |
| I | Cell division control protein 6 | protein | 376 | 30% helix, 4% strand | P09119 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, D, E, I
- MG · Magnesium ion · metal · 4 copies · chains A, D, E, I
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 | 965 | 0.88 | 0.90 | 115 | empty |
| 2 | 533 | 0.88 | 0.94 | 72 | empty |
| 3 | 1172 | 0.84 | 0.85 | 76 | AGS, MG |
| 4 | 1084 | 0.84 | 0.85 | 102 | AGS, MG |
| 5 | 1026 | 0.82 | 0.83 | 98 | empty |
Interfaces
31 interfaces between chains.
- B–C · 5299 Ų buried · 52 hydrogen bonds · protein-protein
- A–D · 4588 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 3244 Ų buried · 28 hydrogen bonds · protein-protein
- A–I · 2656 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 2500 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7MCA · Structure of the S. cerevisiae origin recognition complex bound to the replication… · the same entry in another collection · chain I against I, 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
- P32833 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 2 (P32833) · a predicted model of the same protein · chain B against A, TM-score 0.90
- P54790 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 3 (P54790) · a predicted model of the same protein · chain C against A, TM-score 0.89
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 P54784
- Every structure of UniProt P32833
- Every structure of UniProt P54790
- Every structure of UniProt P54791
- Every structure of UniProt P50874
- Every structure of UniProt P38826
- Every structure of UniProt P09119
- Elsewhere: RCSB PDB 7MCA · PDBe 7MCA · UniProt P54784 · UniProt P32833 · UniProt P54790 · UniProt P54791 · UniProt P50874 · UniProt P38826 · UniProt P09119
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