Research workbench
Crystal structure of lactobacillus rhamnosus 4-deoxy-L-threo-5- hexosulose-uronate ketol-isomerase kdui complexed with hepes
Analyse Crystal structure of lactobacillus rhamnosus 4-deoxy-L-threo-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E4S
- Type
- protein
- Length
- 1,646 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-dehydro-4-deoxy-D-glucuronate isomerase
- EC
- 5.3.1.17
- UniProt
- A0A508YKK7
- Ligands
- ZN
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | 5-dehydro-4-deoxy-D-glucuronate isomerase (EC 5.3.1.17) | protein | 279 | 7% helix, 43% strand | A0A508YKK7 |
| D | 5-dehydro-4-deoxy-D-glucuronate isomerase (EC 5.3.1.17) | protein | 260 | 7% helix, 41% strand | A0A508YKK7 |
| E | 5-dehydro-4-deoxy-D-glucuronate isomerase (EC 5.3.1.17) | protein | 270 | 7% helix, 44% strand | A0A508YKK7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 6 copies · chains A, B, C, D, E, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.72 | 0.96 | 21 | empty |
| 2 | 68 | 0.71 | 0.97 | 18 | empty |
| 3 | 267 | 0.66 | 0.82 | 21 | EPE |
| 4 | 50 | 0.65 | 0.95 | 14 | empty |
| 5 | 250 | 0.62 | 0.80 | 24 | EPE |
Interfaces
6 interfaces between chains.
- B–C · 1638 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1628 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 1615 Ų buried · 41 hydrogen bonds · protein-protein
- A–E · 1607 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1595 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 7E4S · Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate… · 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 A0A508YKK7
- Elsewhere: RCSB PDB 7E4S · PDBe 7E4S · UniProt A0A508YKK7
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