MolNFT v1 · #94117 · protein
Crystal structure of chmj, a 3'-monoepimerase apoenzyme from streptomyces bikiniensis
4HN0 · Putative 3-epimerase in D-allose pathway: “Crystal structure of chmj, a 3'-monoepimerase apoenzyme from streptomyces bikiniensis”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.76). MolNFT v1 #94117 on GenesisL1…
- PDB
- 4HN0
- Type
- protein
- Length
- 791 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
- CL
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative 3-epimerase in D-allose pathway | protein | 198 | 16% helix, 39% strand | Q5SFD1 |
| D | Putative 3-epimerase in D-allose pathway | protein | 197 | 16% helix, 40% strand | Q5SFD1 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 12 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 | 798 | 0.76 | 0.81 | 72 | EDO, CL |
| 2 | 894 | 0.75 | 0.79 | 73 | EDO, CL |
| 3 | 395 | 0.67 | 0.80 | 38 | EDO, CL |
| 4 | 299 | 0.66 | 0.82 | 32 | CL, EDO |
| 5 | 74 | 0.45 | 0.82 | 18 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 1588 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1558 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 334 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 140 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 88 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4HN0 · Crystal Structure of ChmJ, a 3'-monoepimerase apoenzyme from Streptomyces bikiniensis · the same entry in another collection · chain A against A, 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 B 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 4HN0 · PDBe 4HN0 · UniProt Q5SFD1
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