MolNFT v1 · #177054 · protein
Mouse TAB2 nzf in complex with LYS6-linked diubiquitin
7E62: “Mouse TAB2 nzf in complex with LYS6-linked diubiquitin”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.65). MolNFT v1 #177054 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E62
- Type
- protein
- Length
- 359 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; TGF-beta-activated kinase 1 and MAP3K7-binding protein 2
- UniProt
- P62983, Q99K90
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Ubiquitin | protein | 76 | 25% helix, 33% strand | P62983 |
| B | Ubiquitin | protein | 73 | 25% helix, 34% strand | P62983 |
| C, J | TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 | protein | 30 | 0% helix, 20% strand | Q99K90 |
| I | Ubiquitin | protein | 74 | 24% helix, 34% strand | P62983 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains C, J
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.65 | 0.80 | 46 | empty |
| 2 | 263 | 0.58 | 0.78 | 35 | empty |
| 3 | 59 | 0.40 | 0.81 | 16 | empty |
| 4 | 78 | 0.35 | 0.76 | 15 | empty |
Interfaces
9 interfaces between chains.
- B–C · 460 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 450 Ų buried · 4 hydrogen bonds · protein-protein
- I–J · 450 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 404 Ų buried · 5 hydrogen bonds · protein-protein
- H–J · 382 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 7E62 · Mouse TAB2 NZF in complex with Lys6-linked diubiquitin · the same entry in another collection · chain J against J, TM-score 1.00
- P62983 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62983) · a predicted model of the same protein · chain B against A, TM-score 0.96
- 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 0.86
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 P62983
- Every structure of UniProt Q99K90
- Elsewhere: RCSB PDB 7E62 · PDBe 7E62 · UniProt P62983 · UniProt Q99K90
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