Research workbench
Human UBC9 with covalent isopeptide ligand
Analyse Human UBC9 with covalent isopeptide ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SYF
- Type
- protein
- Length
- 658 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sumo-conjugating enzyme UBC9; ACE-leu-arg-leu-arg-gly-cys; ACE-ile-lys-gln-glu
- EC
- 2.3.2.-
- UniProt
- P63279
- Ligands
- ACE
- Pockets
- 8 · best druggability 0.43
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Sumo-conjugating enzyme UBC9 (EC 2.3.2.-) | protein | 153 | 34% helix, 21% strand | P63279 |
| B, C | Sumo-conjugating enzyme UBC9 (EC 2.3.2.-) | protein | 156 | 35% helix, 21% strand | P63279 |
| E, G, I, K | ACE-leu-arg-leu-arg-gly-cys | protein | 6 | 0% helix, 17% strand | — |
| F, H, J, L | ACE-ile-lys-gln-glu | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 8 copies · chains A, E, D, F, B, G, H, C, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.43 | 0.80 | 22 | empty |
| 2 | 93 | 0.43 | 0.79 | 20 | empty |
| 3 | 137 | 0.43 | 0.76 | 25 | empty |
| 4 | 112 | 0.41 | 0.76 | 13 | empty |
| 5 | 74 | 0.37 | 0.77 | 14 | empty |
Interfaces
19 interfaces between chains.
- D–K · 526 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 502 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 499 Ų buried · 6 hydrogen bonds · protein-protein
- C–I · 489 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 396 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 disulfide, 4 isopeptide (covalent ligand, disulfide, isopeptide).
Compared structures
- 6SYF · Human Ubc9 with covalent isopeptide ligand · the same entry in another collection · chain L against L, TM-score 1.00
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 P63279
- Elsewhere: RCSB PDB 6SYF · PDBe 6SYF · UniProt P63279
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