MolNFT v1 · #135784 · protein
1.9 ångström resolution crystal structure of dtdp-4-dehydrorhamnose reductase from yersinia enterocolitica
5U9C: “1.9 ångström resolution crystal structure of dtdp-4-dehydrorhamnose reductase from yersinia enterocolitica”. X-ray diffraction, 3 ligands (BDF, MLT, CL), 17 pockets (best druggability 0.86). MolNFT v1 #135784 on GenesisL1: 3D…
- PDB
- 5U9C
- Type
- protein
- Length
- 1,732 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-4-dehydrorhamnose reductase
- UniProt
- Q56905
- Ligands
- BDF, MLT, CL
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dtdp-4-dehydrorhamnose reductase | protein | 288 | 44% helix, 19% strand | Q56905 |
| B, F | Dtdp-4-dehydrorhamnose reductase | protein | 287 | 44% helix, 20% strand | Q56905 |
| C | Dtdp-4-dehydrorhamnose reductase | protein | 288 | 43% helix, 19% strand | Q56905 |
| D, E | Dtdp-4-dehydrorhamnose reductase | protein | 291 | 42% helix, 20% strand | Q56905 |
Ligands and binding sites
- BDF · beta-D-fructopyranose · ligand · 3 copies · chains A, C, B
- MLT · D-malate · ligand · chains B
- CL · Chloride ion · ion · chains D
- CIT · Citric acid · additive · 4 copies · chains D, E, F
- IMD · Imidazole · additive · 2 copies · chains A, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.86 | 0.87 | 96 | BDF |
| 2 | 1010 | 0.86 | 0.87 | 93 | CIT |
| 3 | 248 | 0.75 | 0.89 | 51 | empty |
| 4 | 228 | 0.74 | 0.89 | 51 | empty |
| 5 | 537 | 0.74 | 0.82 | 69 | empty |
Interfaces
12 interfaces between chains.
- C–F · 704 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 679 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 643 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 626 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 605 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 modified (engineered).
Compared structures
- 5U9C · 1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamnose Reductase from… · 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 Q56905
- Elsewhere: RCSB PDB 5U9C · PDBe 5U9C · UniProt Q56905
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