Research workbench
X-ray crystal structure of the N-terminal btb domain of human KCTD5 protein
Analyse X-ray crystal structure of the N-terminal btb domain of human KCTD5 protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DRZ
- Type
- protein
- Length
- 494 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BTB/POZ domain-containing protein KCTD5
- UniProt
- Q9NXV2
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | BTB/POZ domain-containing protein KCTD5 | protein | 103 | 51% helix, 16% strand | Q9NXV2 |
| C | BTB/POZ domain-containing protein KCTD5 | protein | 96 | 46% helix, 17% strand | Q9NXV2 |
| D | BTB/POZ domain-containing protein KCTD5 | protein | 95 | 44% helix, 17% strand | Q9NXV2 |
| E | BTB/POZ domain-containing protein KCTD5 | protein | 97 | 47% helix, 16% strand | Q9NXV2 |
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 | 930 | 0.75 | 0.78 | 99 | empty |
| 2 | 76 | 0.35 | 0.76 | 19 | empty |
| 3 | 78 | 0.34 | 0.75 | 18 | empty |
| 4 | 70 | 0.33 | 0.75 | 18 | empty |
| 5 | 75 | 0.32 | 0.74 | 18 | empty |
Interfaces
7 interfaces between chains.
- B–C · 794 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 789 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 753 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 729 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3DRZ · X-ray crystal structure of the N-terminal BTB domain of human KCTD5 protein · the same entry in another collection · chain E against E, TM-score 1.00
- Q9NXV2 · AlphaFold monomer V2.0 prediction for BTB/POZ domain-containing protein KCTD5 (Q9NXV2) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9NXV2
- Elsewhere: RCSB PDB 3DRZ · PDBe 3DRZ · UniProt Q9NXV2
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