MolNFT v1 · #125351 · protein
UBA1 in complex with ub-ABPA3 covalent adduct
5L6H · Ubiquitin-activating enzyme E1 1: “UBA1 in complex with ub-ABPA3 covalent adduct”. X-ray diffraction, 4 ligands (6O2, MG, CL), 20 pockets (best druggability 0.77). MolNFT v1 #125351 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5L6H
- Type
- protein
- Length
- 2,235 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-activating enzyme E1 1; Ubiquitin-40S ribosomal protein S31
- EC
- 6.2.1.45
- UniProt
- P22515, P05759
- Ligands
- 6O2, MG, CL, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 1006 | 41% helix, 17% strand | P22515 |
| B, D | Ubiquitin-40S ribosomal protein S31 | protein | 76 | 24% helix, 34% strand | P05759 |
| C | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 1005 | 41% helix, 17% strand | P22515 |
| E | Ubiquitin-40S ribosomal protein S31 | protein | 72 | 25% helix, 31% strand | P05759 |
Ligands and binding sites
- 6O2 · [(2~{R},3~{S},4~{R},5~{R})-5-[6-[(3-ethynylphenyl) amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl sulfamate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains C
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 11 copies · chains A, C
- ACT · Acetate ion · additive · 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 | 754 | 0.77 | 0.81 | 92 | empty |
| 2 | 626 | 0.76 | 0.82 | 93 | empty |
| 3 | 52 | 0.72 | 0.99 | 22 | GOL |
| 4 | 297 | 0.70 | 0.84 | 42 | empty |
| 5 | 340 | 0.65 | 0.80 | 43 | SO4, 6O2 |
Interfaces
5 interfaces between chains.
- A–C · 1883 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1642 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1636 Ų buried · 36 hydrogen bonds · protein-protein
- C–E · 726 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, oxidation).
Compared structures
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 P22515
- Every structure of UniProt P05759
- Elsewhere: RCSB PDB 5L6H · PDBe 5L6H · UniProt P22515 · UniProt P05759
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