Research workbench
Crystal structure of trabid NZF1 in complex with K29 linked di- ubiquitin
Analyse Crystal structure of trabid NZF1 in complex with K29 linked di- ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S1Z
- Type
- protein
- Length
- 498 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Ubiquitin thioesterase ZRANB1
- EC
- 3.4.19.12
- UniProt
- P62987, A6QP16
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ubiquitin | protein | 73 | 16% helix, 36% strand | P62987 |
| D | Ubiquitin | protein | 75 | 24% helix, 29% strand | P62987 |
| E | Ubiquitin | protein | 72 | 21% helix, 38% strand | P62987 |
| F, G, H | Ubiquitin thioesterase ZRANB1 (EC 3.4.19.12) | protein | 27 | 0% helix, 19% strand | A6QP16 |
| J | Ubiquitin thioesterase ZRANB1 (EC 3.4.19.12) | protein | 25 | 0% helix, 16% strand | A6QP16 |
| I | Ubiquitin thioesterase ZRANB1 (EC 3.4.19.12) | protein | 26 | 0% helix, 19% strand | A6QP16 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains F, G, H, J, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.79 | 0.81 | 116 | empty |
| 2 | 117 | 0.62 | 0.87 | 28 | empty |
| 3 | 79 | 0.34 | 0.75 | 18 | empty |
Interfaces
17 interfaces between chains.
- C–G · 420 Ų buried · 3 hydrogen bonds · protein-protein
- A–G · 415 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 395 Ų buried · 3 hydrogen bonds · protein-protein
- E–H · 353 Ų buried · 3 hydrogen bonds · protein-protein
- A–I · 351 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4S1Z · Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin · the same entry in another collection · chain I against I, TM-score 1.00
- P62987 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P62987) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 P62987
- Every structure of UniProt A6QP16
- Elsewhere: RCSB PDB 4S1Z · PDBe 4S1Z · UniProt P62987 · UniProt A6QP16
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