MolNFT v1 · #57502 · protein
Crystal structure of the mouse TAB2-nzf in complex with LYS63-linked di-ubiquitin
3A9J: “Crystal structure of the mouse TAB2-nzf in complex with LYS63-linked di-ubiquitin”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.56). MolNFT v1 #57502 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3A9J
- Type
- protein
- Length
- 185 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Mitogen-activated protein kinase kinase kinase 7- interacting protein 2
- UniProt
- P62991, Q99K90
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin | protein | 76 | 24% helix, 34% strand | P62991 |
| B | Ubiquitin | protein | 77 | 25% helix, 31% strand | P62991 |
| C | Mitogen-activated protein kinase kinase kinase 7- interacting protein 2 | protein | 32 | 0% helix, 22% strand | Q99K90 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.56 | 0.76 | 40 | empty |
| 2 | 78 | 0.33 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 516 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 335 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 142 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 3A9J · Crystal structure of the mouse TAB2-NZF in complex with Lys63-linked di-ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- Q99K90 · AlphaFold monomer V2.0 prediction for TGF-beta-activated kinase 1 and MAP3K7-binding… · 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 P62991
- Every structure of UniProt Q99K90
- Elsewhere: RCSB PDB 3A9J · PDBe 3A9J · UniProt P62991 · UniProt Q99K90
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