MolNFT v1 · #110055 · protein
Structure of dihydrodipicolinate synthase from the commensal bacterium bacteroides thetaiotaomicron at 2.1 a resolution
4XKY: “Structure of dihydrodipicolinate synthase from the commensal bacterium bacteroides thetaiotaomicron at 2.1 a…”. X-ray diffraction, 1 ligand (NA), 10 pockets (best druggability 0.82). MolNFT v1 #110055 on GenesisL1: 3D structure…
- PDB
- 4XKY
- Type
- protein
- Length
- 1,196 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- UniProt
- Q8A3Z0
- Ligands
- NA
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dihydrodipicolinate synthase | protein | 299 | 49% helix, 12% strand | Q8A3Z0 |
| B | Dihydrodipicolinate synthase | protein | 298 | 49% helix, 12% strand | Q8A3Z0 |
| D | Dihydrodipicolinate synthase | protein | 300 | 47% helix, 13% strand | Q8A3Z0 |
Ligands and binding sites
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 | 1090 | 0.82 | 0.83 | 118 | empty |
| 2 | 1116 | 0.81 | 0.82 | 111 | empty |
| 3 | 200 | 0.54 | 0.78 | 23 | empty |
| 4 | 167 | 0.54 | 0.79 | 19 | empty |
| 5 | 141 | 0.51 | 0.79 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1185 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1087 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1062 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1044 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4XKY · Structure of dihydrodipicolinate synthase from the commensal bacterium Bacteroides… · 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 Q8A3Z0
- Elsewhere: RCSB PDB 4XKY · PDBe 4XKY · UniProt Q8A3Z0
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