MolNFT v1 · #135912 · protein
Crystal structure of dhdps from cyanidioschyzon merolae with lysine bound
5UD6 · Dihydrodipicolinate synthase: “Crystal structure of dhdps from cyanidioschyzon merolae with lysine bound”. X-ray diffraction, 2 ligands (LYS, CA), 10 pockets (best druggability 0.72). MolNFT v1 #135912 on GenesisL1: 3D structure…
- PDB
- 5UD6
- Type
- protein
- Length
- 1,194 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- UniProt
- M1V4H9
- Ligands
- LYS, CA
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrodipicolinate synthase | protein | 298 | 49% helix, 13% strand | M1V4H9 |
| C, D | Dihydrodipicolinate synthase | protein | 299 | 48% helix, 13% strand | M1V4H9 |
Ligands and binding sites
- LYS · Lysine · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.72 | 0.84 | 59 | LYS |
| 2 | 400 | 0.69 | 0.81 | 63 | LYS |
| 3 | 244 | 0.56 | 0.78 | 36 | empty |
| 4 | 238 | 0.55 | 0.78 | 39 | empty |
| 5 | 232 | 0.54 | 0.77 | 35 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1405 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1355 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1005 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 989 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5UD6 · Crystal structure of DHDPS from Cyanidioschyzon merolae with lysine bound · the same entry in another collection · chain A 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 M1V4H9
- Elsewhere: RCSB PDB 5UD6 · PDBe 5UD6 · UniProt M1V4H9
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