Research workbench
Structure of the fourth uim (ubiquitin interacting motif) of ANKRD13D in complex with a high affinity ubv (ubiquitin variant)
Analyse Structure of the fourth uim (ubiquitin interacting motif) of ANKRD13D in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RMA
- Type
- protein
- Length
- 94 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin variant; Ankyrin repeat domain-containing protein 13D
- UniProt
- P0CG47, Q6ZTN6
- Ligands
- NA, SO4
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin variant | protein | 75 | 24% helix, 17% strand | P0CG47 |
| C | Ankyrin repeat domain-containing protein 13D | protein | 19 | 74% helix, 0% strand | Q6ZTN6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.60 | 0.77 | 39 | empty |
Interfaces
1 interface between chains.
- A–C · 531 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7RMA · Structure of the fourth UIM (Ubiquitin Interacting Motif) of ANKRD13D in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6ZTN6 · AlphaFold monomer V2.0 prediction for ankyrin repeat domain- containing protein 13D… · a predicted model of the same protein · chain C against A, TM-score 0.74
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 P0CG47
- Every structure of UniProt Q6ZTN6
- Elsewhere: RCSB PDB 7RMA · PDBe 7RMA · UniProt P0CG47 · UniProt Q6ZTN6
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