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The crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N- succinyltransferase from yersinia pestis CO92
Analyse The crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GOS
- Type
- protein
- Length
- 822 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase
- EC
- 2.3.1.117
- UniProt
- Q8ZH69
- Ligands
- MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117) | protein | 270 | 21% helix, 30% strand | Q8ZH69 |
| B, C | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117) | protein | 276 | 22% helix, 29% strand | Q8ZH69 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.80 | 0.84 | 71 | empty |
| 2 | 807 | 0.78 | 0.82 | 77 | empty |
| 3 | 459 | 0.65 | 0.78 | 53 | empty |
| 4 | 55 | 0.41 | 0.82 | 17 | empty |
| 5 | 52 | 0.40 | 0.82 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1893 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1832 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1798 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3GOS · The crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZH69 · AlphaFold monomer V2.0 prediction for 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate… · 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 Q8ZH69
- Elsewhere: RCSB PDB 3GOS · PDBe 3GOS · UniProt Q8ZH69
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