MolNFT v1 · #35391 · protein
The crystal structure of human gins core complex
2E9X · DNA replication complex gins protein PSF1: “The crystal structure of human gins core complex”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.85). MolNFT v1 #35391 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2E9X
- Type
- protein
- Length
- 1,401 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication complex gins protein PSF1; DNA replication complex gins protein PSF2…
- UniProt
- Q14691, Q9Y248, Q9BRX5, Q9BRT9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | DNA replication complex gins protein PSF1 | protein | 144 | 69% helix, 0% strand | Q14691 |
| B, F | DNA replication complex gins protein PSF2 | protein | 175 | 54% helix, 14% strand | Q9Y248 |
| C | Gins complex subunit 3 | protein | 186 | 51% helix, 9% strand | Q9BRX5 |
| D, H | Gins complex subunit 4 | protein | 197 | 58% helix, 13% strand | Q9BRT9 |
| G | Gins complex subunit 3 | protein | 183 | 48% helix, 9% strand | Q9BRX5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, F, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.85 | 0.87 | 108 | empty |
| 2 | 945 | 0.84 | 0.85 | 95 | empty |
| 3 | 479 | 0.80 | 0.87 | 49 | empty |
| 4 | 205 | 0.59 | 0.81 | 43 | empty |
| 5 | 125 | 0.58 | 0.84 | 19 | empty |
Interfaces
18 interfaces between chains.
- F–H · 2095 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 2057 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1805 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1775 Ų buried · 18 hydrogen bonds · protein-protein
- E–H · 1765 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2E9X · The crystal structure of human GINS core complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q9Y248 · AlphaFold monomer V2.0 prediction for DNA replication complex gins protein PSF2 (Q9Y248) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q9BRT9 · AlphaFold monomer V2.0 prediction for DNA replication complex gins protein SLD5 (Q9BRT9) · a predicted model of the same protein · chain D against A, TM-score 0.97
- Q14691 · AlphaFold monomer V2.0 prediction for DNA replication complex gins protein PSF1 (Q14691) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q9BRX5 · AlphaFold monomer V2.0 prediction for DNA replication complex gins protein PSF3 (Q9BRX5) · a predicted model of the same protein · chain G against A, TM-score 0.95
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 Q14691
- Every structure of UniProt Q9Y248
- Every structure of UniProt Q9BRX5
- Every structure of UniProt Q9BRT9
- Elsewhere: RCSB PDB 2E9X · PDBe 2E9X · UniProt Q14691 · UniProt Q9Y248 · UniProt Q9BRX5 · UniProt Q9BRT9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.