MolNFT v1 · #68791 · protein
Dynamic domains of succinyl-COA:3-ketoacid-coenzyme a transferase from pig heart.
3K6M · Succinyl-COA:3-ketoacid-coenzyme a transferase 1…: “Dynamic domains of succinyl-COA:3-ketoacid-coenzyme a transferase from pig heart.”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.85). MolNFT v1 #68791 on…
- PDB
- 3K6M
- Type
- protein
- Length
- 1,854 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-COA:3-ketoacid-coenzyme a transferase 1, mitochondrial
- EC
- 2.8.3.5
- UniProt
- Q29551
- Ligands
- CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-COA:3-ketoacid-coenzyme a transferase 1, mitochondrial (EC 2.8.3.5) | protein | 465 | 22% helix, 32% strand | Q29551 |
| D | Succinyl-COA:3-ketoacid-coenzyme a transferase 1, mitochondrial (EC 2.8.3.5) | protein | 462 | 22% helix, 32% strand | Q29551 |
| C | Succinyl-COA:3-ketoacid-coenzyme a transferase 1, mitochondrial (EC 2.8.3.5) | protein | 466 | 22% helix, 33% strand | Q29551 |
| B | Succinyl-COA:3-ketoacid-coenzyme a transferase 1, mitochondrial (EC 2.8.3.5) | protein | 461 | 22% helix, 32% strand | Q29551 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.85 | 0.97 | 37 | empty |
| 2 | 210 | 0.83 | 0.97 | 32 | empty |
| 3 | 960 | 0.74 | 0.77 | 100 | empty |
| 4 | 589 | 0.74 | 0.81 | 81 | CL |
| 5 | 461 | 0.72 | 0.82 | 58 | empty |
Interfaces
4 interfaces between chains.
- D–C · 2446 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2429 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 164 Ų buried · 1 hydrogen bond · protein-protein
- D–B · 108 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3K6M · Dynamic domains of Succinyl-CoA:3-ketoacid-coenzyme A transferase from pig heart. · the same entry in another collection · chain B against B, TM-score 1.00
- Q29551 · AlphaFold monomer V2.0 prediction for succinyl-COA:3-ketoacid coenzyme a transferase 1… · a predicted model of the same protein · chain D 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 Q29551
- Elsewhere: RCSB PDB 3K6M · PDBe 3K6M · UniProt Q29551
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