MolNFT v1 · #59959 · protein
Crystal structure of the co-expressed succinyl-CoA transferase a and B complex from bacillus subtilis
3CDK · Succinyl-COA:3-ketoacid-coenzyme a transferase subunit a: “Crystal structure of the co-expressed succinyl-CoA transferase a and B complex from bacillus subtilis”. X-ray diffraction, 9 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 3CDK
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinyl-COA:3-ketoacid-coenzyme a transferase subunit a…
- EC
- 2.8.3.5
- UniProt
- P42315, P42316
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinyl-COA:3-ketoacid-coenzyme a transferase subunit a (EC 2.8.3.5) | protein | 229 | 24% helix, 31% strand | P42315 |
| B | Succinyl-COA:3-ketoacid-coenzyme a transferase subunit B (EC 2.8.3.5) | protein | 212 | 19% helix, 30% strand | P42316 |
| C | Succinyl-COA:3-ketoacid-coenzyme a transferase subunit a (EC 2.8.3.5) | protein | 229 | 25% helix, 31% strand | P42315 |
| D | Succinyl-COA:3-ketoacid-coenzyme a transferase subunit B (EC 2.8.3.5) | protein | 200 | 20% helix, 27% strand | P42316 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.83 | 0.96 | 34 | empty |
| 2 | 393 | 0.70 | 0.82 | 63 | empty |
| 3 | 386 | 0.67 | 0.80 | 55 | empty |
| 4 | 256 | 0.59 | 0.79 | 44 | empty |
| 5 | 155 | 0.42 | 0.75 | 34 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2116 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2081 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 956 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 730 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 730 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3CDK · Crystal structure of the co-expressed succinyl-CoA transferase A and B complex from… · the same entry in another collection · chain D against D, TM-score 1.00
- P42316 · AlphaFold monomer V2.0 prediction for probable succinyl- COA:3-ketoacid coenzyme a… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P42315 · AlphaFold monomer V2.0 prediction for probable succinyl- COA:3-ketoacid coenzyme a… · a predicted model of the same protein · chain A 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 P42315
- Every structure of UniProt P42316
- Elsewhere: RCSB PDB 3CDK · PDBe 3CDK · UniProt P42315 · UniProt P42316
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