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Crystal structure of chmj, a 3'-monoepimerase from streptomyces bikiniensis in complex with dtdp-quinovose
Analyse Crystal structure of chmj, a 3'-monoepimerase from streptomyces bikiniensis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HMZ
- Type
- protein
- Length
- 797 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
- 18T
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative 3-epimerase in D-allose pathway | protein | 198 | 17% helix, 39% strand | Q5SFD1 |
| B | Putative 3-epimerase in D-allose pathway | protein | 199 | 18% helix, 38% strand | Q5SFD1 |
| C, D | Putative 3-epimerase in D-allose pathway | protein | 200 | 18% helix, 39% strand | Q5SFD1 |
Ligands and binding sites
- 18T · [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.76 | 0.83 | 62 | EDO, 18T |
| 2 | 601 | 0.75 | 0.82 | 64 | 18T, EDO |
| 3 | 286 | 0.65 | 0.82 | 38 | EDO, 18T |
| 4 | 265 | 0.65 | 0.82 | 40 | 18T, EDO |
| 5 | 72 | 0.45 | 0.82 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1591 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1450 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 337 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 139 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4HMZ · Crystal Structure of ChmJ, a 3'-monoepimerase from Streptomyces bikiniensis in complex… · 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 0.99
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 4HMZ · PDBe 4HMZ · UniProt Q5SFD1
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