Research workbench
Structure of the active form of human origin recognition complex and its ATPase motor module
Analyse Structure of the active form of human origin recognition complex and its ATPase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UJM
- Type
- protein
- Length
- 1,928 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
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Origin recognition complex subunit 1 | protein | 337 | 54% helix, 10% strand | Q13415 |
| B | Origin recognition complex subunit 2 | protein | 287 | 47% helix, 13% strand | Q13416 |
| C | Origin recognition complex subunit 3 | protein | 553 | 62% helix, 5% strand | Q9UBD5 |
| D | Origin recognition complex subunit 4 | protein | 394 | 55% helix, 9% strand | O43929 |
| E | Origin recognition complex subunit 5 | protein | 357 | 50% helix, 10% strand | O43913 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, E
- MG · Magnesium ion · metal · 2 copies · chains 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.86 | 0.93 | 62 | empty |
| 2 | 1105 | 0.81 | 0.82 | 121 | empty |
| 3 | 700 | 0.80 | 0.84 | 86 | empty |
| 4 | 575 | 0.80 | 0.86 | 64 | ATP, MG |
| 5 | 1148 | 0.79 | 0.81 | 96 | ATP |
Interfaces
7 interfaces between chains.
- A–D · 2927 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 2663 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1721 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 1162 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 487 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5UJM · Structure of the active form of human Origin Recognition Complex and its ATPase motor… · the same entry in another collection · chain E against E, TM-score 1.00
- 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
- 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
- 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 0.93
- 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 0.62
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 5UJM · PDBe 5UJM · UniProt Q13415 · UniProt Q13416 · UniProt Q9UBD5 · UniProt O43929 · UniProt O43913
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