Research workbench
Branched LYS48- and LYS63-linked tri-ubiquitin (K48-K63-UB3) in complex with synthetic nanobody NBSL3
Analyse Branched LYS48- and LYS63-linked tri-ubiquitin (K48-K63-UB3) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NBB
- Type
- protein
- Length
- 683 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-B; Synthetic nanobody NBSL3
- UniProt
- J3QS39
- Ligands
- MG, NA, CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Polyubiquitin-B | protein | 71 | 25% helix, 32% strand | J3QS39 |
| B, C, F, G | Polyubiquitin-B | protein | 76 | 24% helix, 33% strand | J3QS39 |
| D | Synthetic nanobody NBSL3 | protein | 119 | 6% helix, 55% strand | — |
| H | Synthetic nanobody NBSL3 | protein | 118 | 6% helix, 57% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, H, F, G
- NA · Sodium ion · metal · 2 copies · chains C, F, G, H
- CL · Chloride ion · ion · 7 copies · chains C, D, E, F, G, H
- GOL · Glycerol · additive · 2 copies · chains B, C, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.74 | 0.78 | 83 | CL |
| 2 | 167 | 0.49 | 0.78 | 29 | GOL, MG |
| 3 | 154 | 0.49 | 0.78 | 31 | GOL, MG, CL |
| 4 | 66 | 0.38 | 0.78 | 17 | empty |
| 5 | 71 | 0.38 | 0.78 | 17 | empty |
Interfaces
17 interfaces between chains.
- C–D · 913 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 893 Ų buried · 14 hydrogen bonds · protein-protein
- E–H · 547 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 542 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 465 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide, 1 disulfide (isopeptide, disulfide).
Compared structures
- 7NBB · Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic… · the same entry in another collection · chain A against A, 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 J3QS39
- Elsewhere: RCSB PDB 7NBB · PDBe 7NBB · UniProt J3QS39
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