Research workbench
Crystal structure of H60N/Y130F double mutant of chmj, a 3'- monoepimerase from streptomyces bikiniensis in complex with dtdp
Analyse Crystal structure of H60N/Y130F double mutant of chmj, a 3'- monoepimerase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HN1
- Type
- protein
- Length
- 799 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 3-epimerase in D-allose pathway
- UniProt
- Q5SFD1
- Ligands
- TYD, THM, TDR
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative 3-epimerase in D-allose pathway | protein | 199 | 18% helix, 39% strand | Q5SFD1 |
| C | Putative 3-epimerase in D-allose pathway | protein | 201 | 18% helix, 38% strand | Q5SFD1 |
| D | Putative 3-epimerase in D-allose pathway | protein | 200 | 18% helix, 38% strand | Q5SFD1 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- THM · Thymidine · ligand · 2 copies · chains A, B
- TDR · Thymine · ligand · 2 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.78 | 0.81 | 80 | EDO, TYD |
| 2 | 879 | 0.76 | 0.80 | 81 | EDO, TYD |
| 3 | 341 | 0.68 | 0.82 | 47 | TYD, EDO |
| 4 | 330 | 0.66 | 0.81 | 34 | EDO, TYD |
| 5 | 65 | 0.45 | 0.82 | 19 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 1599 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1491 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 350 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 143 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 64 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4HN1 · Crystal Structure of H60N/Y130F double mutant of ChmJ, a 3'-monoepimerase from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q5SFD1 · AlphaFold monomer V2.0 prediction for dtdp-4-dehydro-6-deoxyglucose 3-epimerase (Q5SFD1) · a predicted model of the same protein · chain A 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 Q5SFD1
- Elsewhere: RCSB PDB 4HN1 · PDBe 4HN1 · UniProt Q5SFD1
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