Research workbench
Three-dimensional structure of tetrahydrodipicolinate-N- succinlytransferase
Analyse Three-dimensional structure of tetrahydrodipicolinate-N- succinlytransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TDT
- Type
- protein
- Length
- 764 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrahydrodipicolinate-N-succinlytransferase
- UniProt
- P56220
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetrahydrodipicolinate-N-succinlytransferase | protein | 256 | 20% helix, 32% strand | P56220 |
| B | Tetrahydrodipicolinate-N-succinlytransferase | protein | 255 | 20% helix, 31% strand | P56220 |
| C | Tetrahydrodipicolinate-N-succinlytransferase | protein | 253 | 19% helix, 32% strand | P56220 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.77 | 0.79 | 123 | empty |
| 2 | 521 | 0.69 | 0.79 | 53 | empty |
| 3 | 56 | 0.69 | 0.96 | 27 | empty |
| 4 | 83 | 0.45 | 0.81 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1630 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1615 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1610 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1TDT · Three-dimensional structure of tetrahydrodipicolinate-N-succinyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
- P56220 · 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 1.00
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 P56220
- Elsewhere: RCSB PDB 1TDT · PDBe 1TDT · UniProt P56220
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