MolNFT v1 · #23319 · protein
Crystal structure of diaminopimelate decarboxylase from M. jannaschii in co-complex with L-lysine
1TWI: “Crystal structure of diaminopimelate decarboxylase from M. jannaschii in co-complex with L-lysine”. X-ray diffraction, 3 ligands (LYS, PLP, MG), 20 pockets (best druggability 0.81). MolNFT v1 #23319 on GenesisL1: 3D structure…
- PDB
- 1TWI
- Type
- protein
- Length
- 1,736 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate decarboxylase
- EC
- 4.1.1.20
- UniProt
- Q58497
- Ligands
- LYS, PLP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 434 | 35% helix, 26% strand | Q58497 |
Ligands and binding sites
- LYS · Lysine · ligand · 6 copies · chains A, B, C, D
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.81 | 0.94 | 50 | empty |
| 2 | 231 | 0.81 | 0.94 | 52 | empty |
| 3 | 295 | 0.68 | 0.83 | 44 | LYS, PLP |
| 4 | 744 | 0.67 | 0.75 | 59 | empty |
| 5 | 365 | 0.67 | 0.80 | 48 | PLP, LYS |
Interfaces
3 interfaces between chains.
- C–D · 4143 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 4070 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 114 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1TWI · Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q58497 · AlphaFold monomer V2.0 prediction for diaminopimelate decarboxylase (Q58497) · a predicted model of the same protein · chain C 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 Q58497
- Elsewhere: RCSB PDB 1TWI · PDBe 1TWI · UniProt Q58497
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