MolNFT v1 · #169832 · protein
Structure of SUMO1-ML00789344 adduct bound to sae
6XOH · Sumo-activating enzyme subunit 1: “Structure of SUMO1-ML00789344 adduct bound to sae”. X-ray diffraction, 3 ligands (VB7, ZN, SO4), 12 pockets (best druggability 0.72). MolNFT v1 #169832 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6XOH
- Type
- protein
- Length
- 853 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
- VB7, ZN, SO4
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sumo-activating enzyme subunit 1 | protein | 311 | 45% helix, 21% strand | Q9UBE0 |
| B | Sumo-activating enzyme subunit 2 (EC 2.3.2.-) | protein | 490 | 40% helix, 16% strand | Q9UBT2 |
| C | Small ubiquitin-related modifier 1 | protein | 52 | 13% helix, 42% strand | P63165 |
Ligands and binding sites
- VB7 · {(1R,2S,4R)-4-[(5-{4-[(1R)-3,4-dihydro-1H-2-benzopyran-1-yl]thiophene-2-carbonyl}pyrimidin-4-yl)amino]-2-hydroxycyclopentyl}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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.72 | 0.81 | 72 | empty |
| 2 | 346 | 0.70 | 0.83 | 50 | empty |
| 3 | 317 | 0.64 | 0.80 | 43 | SO4, VB7 |
| 4 | 110 | 0.62 | 0.87 | 26 | empty |
| 5 | 142 | 0.50 | 0.79 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2532 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 949 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6XOH · Structure of SUMO1-ML00789344 adduct bound to SAE · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.99
- 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
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 6XOH · PDBe 6XOH · UniProt Q9UBE0 · UniProt Q9UBT2 · UniProt P63165
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