MolNFT v1 · #181966 · protein + DNA
Structure of the S. cerevisiae origin recognition complex bound to the replication initiator CDC6 and the ARS1 origin DNA.
7MCA · Origin recognition complex subunit 1: “Structure of the S. cerevisiae origin recognition complex bound to the replication initiator CDC6 and the…”. Electron microscopy, 2 ligands (AGS, MG), 20 pockets (best druggability 0.88).…
- 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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