Research workbench
Structure of the bacillus anthracis tetrahydropicolinate succinyltransferase
Analyse Structure of the bacillus anthracis tetrahydropicolinate succinyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R8Y
- Type
- protein
- Length
- 1,234 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- acetyltransferase
- EC
- 2.3.1.89
- UniProt
- Q81MQ2
- Ligands
- CA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- acetyltransferase (EC 2.3.1.89) | protein | 203 | 6% helix, 38% strand | Q81MQ2 |
| B | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- acetyltransferase (EC 2.3.1.89) | protein | 213 | 11% helix, 35% strand | Q81MQ2 |
| C | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- acetyltransferase (EC 2.3.1.89) | protein | 201 | 6% helix, 35% strand | Q81MQ2 |
| E | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- acetyltransferase (EC 2.3.1.89) | protein | 212 | 11% helix, 33% strand | Q81MQ2 |
| F | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- acetyltransferase (EC 2.3.1.89) | protein | 202 | 6% helix, 36% strand | Q81MQ2 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.79 | 0.99 | 21 | empty |
| 2 | 898 | 0.77 | 0.80 | 107 | CA |
| 3 | 79 | 0.77 | 0.99 | 20 | empty |
| 4 | 1103 | 0.74 | 0.77 | 71 | CA |
| 5 | 709 | 0.74 | 0.79 | 61 | CA |
Interfaces
9 interfaces between chains.
- D–F · 1442 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1421 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1407 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1406 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1406 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3R8Y · Structure of the Bacillus anthracis tetrahydropicolinate succinyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
- Q81MQ2 · AlphaFold monomer V2.0 prediction for 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate… · a predicted model of the same protein · chain B 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 Q81MQ2
- Elsewhere: RCSB PDB 3R8Y · PDBe 3R8Y · UniProt Q81MQ2
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