MolNFT v1 · #100042 · protein
Dihydrodipicolinate synthase from C. jejuni, Y110F mutation with pyruvate and lysine
4MLR: “Dihydrodipicolinate synthase from C. jejuni, Y110F mutation with pyruvate and lysine”. X-ray diffraction, 1 ligand (LYS), 19 pockets (best druggability 0.79). MolNFT v1 #100042 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4MLR
- Type
- protein
- Length
- 2,363 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- Q9PPB4
- Ligands
- LYS
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, G | Dihydrodipicolinate synthase (EC 4.3.3.7) | protein | 296 | 47% helix, 14% strand | Q9PPB4 |
| C, H | Dihydrodipicolinate synthase (EC 4.3.3.7) | protein | 295 | 47% helix, 14% strand | Q9PPB4 |
| D | Dihydrodipicolinate synthase (EC 4.3.3.7) | protein | 295 | 46% helix, 14% strand | Q9PPB4 |
| E | Dihydrodipicolinate synthase (EC 4.3.3.7) | protein | 294 | 48% helix, 14% strand | Q9PPB4 |
Ligands and binding sites
- LYS · Lysine · ligand · 8 copies · chains A, D, B, C, E, F, G, H
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, D, E, G
- PGE · Triethylene glycol · additive · 5 copies · chains B, C, E, F, H
- ACT · Acetate ion · additive · 2 copies · chains A, C, E, F
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.79 | 0.90 | 50 | LYS, ACT |
| 2 | 299 | 0.78 | 0.90 | 49 | LYS |
| 3 | 366 | 0.76 | 0.87 | 46 | LYS |
| 4 | 257 | 0.76 | 0.89 | 38 | LYS |
| 5 | 415 | 0.56 | 0.74 | 53 | empty |
Interfaces
10 interfaces between chains.
- G–H · 1517 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1502 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1495 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1481 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1056 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard).
Compared structures
- 4MLR · dihydrodipicolinate synthase from C. jejuni, Y110F mutation with pyruvate and Lysine · the same entry in another collection · chain E against E, TM-score 1.00
- Q9PPB4 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9PPB4) · a predicted model of the same protein · 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 Q9PPB4
- Elsewhere: RCSB PDB 4MLR · PDBe 4MLR · UniProt Q9PPB4
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