MolNFT v1 · #109899 · protein
Crystal structure of the eukaryotic origin recognition complex
4XGC · Origin recognition complex subunit 2: “Crystal structure of the eukaryotic origin recognition complex”. X-ray diffraction, 2 ligands (K, CL), 20 pockets (best druggability 0.85). MolNFT v1 #109899 on GenesisL1: 3D structure, binding…
- PDB
- 4XGC
- Type
- protein
- Length
- 2,056 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Origin recognition complex subunit 2; Origin recognition complex subunit 3; Origin…
- EC
- 3.6.1.15
- UniProt
- Q24168, Q7K2L1, Q24169, O16810, Q9Y1B2, Q9W102
- Ligands
- K, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Origin recognition complex subunit 2 | protein | 281 | 51% helix, 11% strand | Q24168 |
| C | Origin recognition complex subunit 3 | protein | 567 | 66% helix, 8% strand | Q7K2L1 |
| E | Origin recognition complex subunit 5 | protein | 402 | 51% helix, 11% strand | Q24169 |
| A | Origin recognition complex subunit 1 | protein | 310 | 60% helix, 11% strand | O16810 |
| G | Origin recognition complex subunit 2 | protein | 37 | 35% helix, 0% strand | — |
| F | Origin recognition complex subunit 6 | protein | 19 | 84% helix, 0% strand | Q9Y1B2 |
| D | Origin recognition complex subunit 4 (EC 3.6.1.15) | protein | 440 | 56% helix, 9% strand | Q9W102 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.85 | 0.87 | 87 | empty |
| 2 | 792 | 0.81 | 0.84 | 105 | K |
| 3 | 135 | 0.80 | 0.97 | 27 | empty |
| 4 | 993 | 0.77 | 0.79 | 85 | empty |
| 5 | 440 | 0.77 | 0.86 | 65 | CL |
Interfaces
15 interfaces between chains.
- E–D · 2932 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2100 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 1955 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1306 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 838 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4XGC · Crystal structure of the eukaryotic origin recognition complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q24168 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 2 (Q24168) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q24169 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 5 (Q24169) · a predicted model of the same protein · chain E against A, TM-score 0.94
- Q9Y1B2 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 6 (Q9Y1B2) · a predicted model of the same protein · chain F against A, TM-score 0.75
- O16810 · AlphaFold monomer V2.0 prediction for origin recognition complex subunit 1 (O16810) · a predicted model of the same protein · chain A 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 Q24168
- Every structure of UniProt Q7K2L1
- Every structure of UniProt Q24169
- Every structure of UniProt O16810
- Every structure of UniProt Q9Y1B2
- Every structure of UniProt Q9W102
- Elsewhere: RCSB PDB 4XGC · PDBe 4XGC · UniProt Q24168 · UniProt Q7K2L1 · UniProt Q24169 · UniProt O16810 · UniProt Q9Y1B2 · UniProt Q9W102
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