MolNFT v1 · #143023 · protein
Crystal structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase from acinetobacter baumannii
6AMY: “Crystal structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase from acinetobacter…”. X-ray diffraction, 8 pockets (best druggability 0.73). MolNFT v1 #143023 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6AMY
- Type
- protein
- Length
- 784 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
- Q5DL43
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 19% 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 | 266 | 20% helix, 29% strand | Q5DL43 |
| B | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117) | protein | 258 | 19% helix, 31% strand | Q5DL43 |
| C | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- succinyltransferase (EC 2.3.1.117) | protein | 260 | 19% helix, 31% strand | Q5DL43 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.73 | 0.97 | 19 | empty |
| 2 | 508 | 0.73 | 0.81 | 56 | empty |
| 3 | 573 | 0.70 | 0.79 | 62 | empty |
| 4 | 507 | 0.66 | 0.77 | 47 | empty |
| 5 | 90 | 0.48 | 0.82 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1824 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1698 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1691 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6AMY · Crystal structure of a 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5DL43 · 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 0.99
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 Q5DL43
- Elsewhere: RCSB PDB 6AMY · PDBe 6AMY · UniProt Q5DL43
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