Research workbench
Crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N- succinyltransferase from bartonella henselae
Analyse 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
- 6WQM
- Type
- protein
- Length
- 1,681 residues
- Chains
- 6
- 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
- Q6G549
- Ligands
- CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117) | protein | 280 | 24% helix, 28% strand | Q6G549 |
| B | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117) | protein | 279 | 23% helix, 28% strand | Q6G549 |
| C | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117) | protein | 280 | 24% helix, 29% strand | Q6G549 |
| D, E | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117) | protein | 281 | 23% helix, 28% strand | Q6G549 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.85 | 0.95 | 71 | CL |
| 2 | 345 | 0.85 | 0.94 | 69 | CL |
| 3 | 127 | 0.79 | 0.97 | 30 | empty |
| 4 | 121 | 0.78 | 0.96 | 23 | empty |
| 5 | 653 | 0.75 | 0.81 | 55 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1797 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1762 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1759 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1753 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1729 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6WQM · Crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from… · the same entry in another collection · chain F against F, TM-score 1.00
- Q6G549 · AlphaFold monomer V2.0 prediction for 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate… · a predicted model of the same protein · chain F against A, TM-score 0.99
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 Q6G549
- Elsewhere: RCSB PDB 6WQM · PDBe 6WQM · UniProt Q6G549
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