Research workbench
Structure of the C-terminal motor domain of KAR3 from candida glabrata
Analyse Structure of the C-terminal motor domain of KAR3 from candida glabrata in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GKR
- Type
- protein
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neck and C-terminal motor domain of KAR3
- UniProt
- Q6FVW6
- Ligands
- ADP, MG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neck and C-terminal motor domain of KAR3 | protein | 296 | 35% helix, 30% strand | Q6FVW6 |
| B | Neck and C-terminal motor domain of KAR3 | protein | 307 | 36% helix, 30% strand | Q6FVW6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.73 | 0.76 | 93 | EDO |
| 2 | 155 | 0.56 | 0.82 | 25 | empty |
| 3 | 89 | 0.49 | 0.82 | 21 | empty |
| 4 | 129 | 0.43 | 0.76 | 33 | MG |
| 5 | 123 | 0.42 | 0.77 | 32 | MG, ADP |
Interfaces
1 interface between chains.
- A–B · 363 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4GKR · Structure of the C-terminal motor domain of Kar3 from Candida glabrata · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6FVW6
- Elsewhere: RCSB PDB 4GKR · PDBe 4GKR · UniProt Q6FVW6
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