Research workbench
X-ray crystal structure of human KCTD5 protein crystallized in low- salt buffer
Analyse X-ray crystal structure of human KCTD5 protein crystallized in low- salt buffer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DRY
- Type
- protein
- Length
- 844 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
- 16 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BTB/POZ domain-containing protein KCTD5 | protein | 166 | 38% helix, 19% strand | Q9NXV2 |
| B, E | BTB/POZ domain-containing protein KCTD5 | protein | 164 | 36% helix, 23% strand | Q9NXV2 |
| C | BTB/POZ domain-containing protein KCTD5 | protein | 178 | 36% helix, 20% strand | Q9NXV2 |
| D | BTB/POZ domain-containing protein KCTD5 | protein | 172 | 33% helix, 20% strand | Q9NXV2 |
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.76 | 0.79 | 61 | empty |
| 2 | 1171 | 0.73 | 0.76 | 101 | empty |
| 3 | 176 | 0.44 | 0.74 | 26 | empty |
| 4 | 128 | 0.39 | 0.74 | 21 | empty |
| 5 | 112 | 0.37 | 0.74 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1577 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1570 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1495 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 1484 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1435 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3DRY · X-ray crystal structure of human KCTD5 protein crystallized in low-salt buffer · 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 0.78
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 Q9NXV2
- Elsewhere: RCSB PDB 3DRY · PDBe 3DRY · UniProt Q9NXV2
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