Research workbench
Crystal structure of mvca-UBE2N-ub complex from legionella pneumophila
Analyse Crystal structure of mvca-UBE2N-ub complex from legionella pneumophila in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JKY
- Type
- protein
- Length
- 1,213 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mvca; Ubiquitin-conjugating enzyme E2 N; Ub
- EC
- 2.3.2.23
- UniProt
- Q5ZTL3, P61088, A0A3P7ZMV6
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mvca | protein | 384 | 50% helix, 14% strand | Q5ZTL3 |
| B | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 149 | 32% helix, 16% strand | P61088 |
| C | Ub | protein | 76 | 24% helix, 33% strand | A0A3P7ZMV6 |
| D | Mvca | protein | 381 | 52% helix, 14% strand | Q5ZTL3 |
| E | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 148 | 32% helix, 15% strand | P61088 |
| F | Ub | protein | 75 | 24% helix, 35% strand | A0A3P7ZMV6 |
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.83 | 0.85 | 117 | empty |
| 2 | 410 | 0.79 | 0.88 | 45 | empty |
| 3 | 1194 | 0.78 | 0.80 | 118 | empty |
| 4 | 590 | 0.77 | 0.83 | 51 | empty |
| 5 | 460 | 0.74 | 0.83 | 50 | empty |
Interfaces
10 interfaces between chains.
- D–F · 1496 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1470 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1379 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1376 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 255 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 6JKY · Crystal structure of MvcA-UBE2N-Ub complex from Legionella pneumophila · the same entry in another collection · chain F against F, TM-score 1.00
- P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q5ZTL3
- Every structure of UniProt P61088
- Every structure of UniProt A0A3P7ZMV6
- Elsewhere: RCSB PDB 6JKY · PDBe 6JKY · UniProt Q5ZTL3 · UniProt P61088 · UniProt A0A3P7ZMV6
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