Research workbench
Orc-O1AAA: human origin recognition complex (orc) with DYNAMIC/UNRESOLVED ORC2 wh
Analyse Orc-O1AAA: human origin recognition complex (orc) with DYNAMIC/UNRESOLVED ORC2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JPO
- Type
- protein
- Length
- 1,966 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Origin recognition complex subunit 1; Origin recognition complex subunit 2; Origin…
- UniProt
- Q13415, Q13416, Q9UBD5, O43929, O43913
- Ligands
- ATP, MG, K
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Origin recognition complex subunit 1 | protein | 352 | 54% helix, 10% strand | Q13415 |
| B | Origin recognition complex subunit 2 | protein | 209 | 37% helix, 13% strand | Q13416 |
| C | Origin recognition complex subunit 3 | protein | 594 | 60% helix, 6% strand | Q9UBD5 |
| D | Origin recognition complex subunit 4 | protein | 406 | 55% helix, 9% strand | O43929 |
| E | Origin recognition complex subunit 5 | protein | 405 | 48% helix, 8% strand | O43913 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, E
- MG · Magnesium ion · metal · 3 copies · chains A, D, E
- K · Potassium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.84 | 0.88 | 72 | empty |
| 2 | 1080 | 0.82 | 0.83 | 92 | ATP, MG |
| 3 | 755 | 0.79 | 0.83 | 71 | ATP, MG |
| 4 | 618 | 0.75 | 0.82 | 62 | ATP, MG |
| 5 | 99 | 0.75 | 0.96 | 24 | empty |
Interfaces
7 interfaces between chains.
- B–C · 3415 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 2821 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 2594 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 2084 Ų buried · 18 hydrogen bonds · protein-protein
- B–E · 1044 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7JPO · ORC-O1AAA: Human Origin Recognition Complex (ORC) with dynamic/unresolved ORC2 WH · the same entry in another collection · chain E against E, TM-score 1.00
- Q9UBD5 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 3 (Q9UBD5) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q13415 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 1 (Q13415) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q13416 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 2 (Q13416) · a predicted model of the same protein · chain B against A, TM-score 0.96
- O43929 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 4 (O43929) · a predicted model of the same protein · chain D against A, TM-score 0.94
- O43913 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 5 (O43913) · a predicted model of the same protein · chain E against A, TM-score 0.93
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 Q13415
- Every structure of UniProt Q13416
- Every structure of UniProt Q9UBD5
- Every structure of UniProt O43929
- Every structure of UniProt O43913
- Elsewhere: RCSB PDB 7JPO · PDBe 7JPO · UniProt Q13415 · UniProt Q13416 · UniProt Q9UBD5 · UniProt O43929 · UniProt O43913
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