MolNFT v1 · #158905 · protein
S. pombe ubiquitin E1~UBIQUITIN-AMP tetrahedral intermediate mimic
6O83 · Ubiquitin-activating enzyme E1 1: “S. pombe ubiquitin E1~UBIQUITIN-AMP tetrahedral intermediate mimic”. X-ray diffraction, 2 ligands (VMX, CA), 20 pockets (best druggability 0.84). MolNFT v1 #158905 on GenesisL1: 3D structure…
- PDB
- 6O83
- Type
- protein
- Length
- 2,059 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-activating enzyme E1 1; Ubiquitin-60S ribosomal protein L40
- EC
- 6.2.1.45
- UniProt
- O94609, P0CH07
- Ligands
- VMX, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 954 | 38% helix, 18% strand | O94609 |
| B, D | Ubiquitin-60S ribosomal protein L40 | protein | 75 | 20% helix, 32% strand | P0CH07 |
| C | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 955 | 39% helix, 19% strand | O94609 |
Ligands and binding sites
- VMX · 5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine · ligand · 2 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 11 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C
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 | 1020 | 0.84 | 0.85 | 110 | VMX |
| 2 | 525 | 0.80 | 0.87 | 73 | VMX |
| 3 | 814 | 0.79 | 0.82 | 73 | empty |
| 4 | 705 | 0.76 | 0.81 | 72 | empty |
| 5 | 514 | 0.76 | 0.84 | 61 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1647 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1629 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 415 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6O83 · S. pombe ubiquitin E1~ubiquitin-AMP tetrahedral intermediate mimic · the same entry in another collection · chain A against A, TM-score 1.00
- P0CH07 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P0CH07) · a predicted model of the same protein · chain B against A, TM-score 0.92
- O94609 · AlphaFold monomer V2.0 prediction for ubiquitin-activating enzyme E1 1 (O94609) · a predicted model of the same protein · chain C against A, TM-score 0.78
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 O94609
- Every structure of UniProt P0CH07
- Elsewhere: RCSB PDB 6O83 · PDBe 6O83 · UniProt O94609 · UniProt P0CH07
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