Research workbench
Structure of SUMO1-ML786519 adduct bound to sae
Analyse Structure of SUMO1-ML786519 adduct bound to sae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XOG
- Type
- protein
- Length
- 873 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sumo-activating enzyme subunit 1; Sumo-activating enzyme subunit 2; Small…
- EC
- 2.3.2.-
- UniProt
- Q9UBE0, Q9UBT2, P63165
- Ligands
- VAY, ZN, SO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sumo-activating enzyme subunit 1 | protein | 311 | 46% helix, 21% strand | Q9UBE0 |
| B | Sumo-activating enzyme subunit 2 (EC 2.3.2.-) | protein | 500 | 42% helix, 15% strand | Q9UBT2 |
| C | Small ubiquitin-related modifier 1 | protein | 62 | 6% helix, 35% strand | P63165 |
Ligands and binding sites
- VAY · {(1R,2R,3S,4R)-4-[(5-{4-[(1S)-1-(6-bromopyridin-2-yl)-1-hydroxyethyl]thiophene-2-carbonyl}pyrimidin-4-yl) amino]-2,3-dihydroxycyclopentyl}methyl sulfamate · ligand · chains B, C
- ZN · Zinc ion · metal · chains B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.73 | 0.98 | 21 | empty |
| 2 | 702 | 0.73 | 0.79 | 78 | empty |
| 3 | 442 | 0.73 | 0.83 | 48 | empty |
| 4 | 343 | 0.66 | 0.81 | 44 | SO4, VAY |
| 5 | 61 | 0.42 | 0.81 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2513 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1029 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6XOG · Structure of SUMO1-ML786519 adduct bound to SAE · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBE0 · AlphaFold monomer V2.0 prediction for sumo-activating enzyme subunit 1 (Q9UBE0) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9UBT2 · AlphaFold monomer V2.0 prediction for sumo-activating enzyme subunit 2 (Q9UBT2) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P63165 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 1 (P63165) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 Q9UBE0
- Every structure of UniProt Q9UBT2
- Every structure of UniProt P63165
- Elsewhere: RCSB PDB 6XOG · PDBe 6XOG · UniProt Q9UBE0 · UniProt Q9UBT2 · UniProt P63165
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