Research workbench
Crystal structure of 0.5M urea unfolded yage, a kdg aldolase protein in complex with pyruvate
Analyse Crystal structure of 0.5M urea unfolded yage, a kdg aldolase protein in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U4M
- Type
- protein
- Length
- 1,192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yage
- Ligands
- URE, PYR
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Yage | protein | 298 | 51% helix, 12% strand | — |
Ligands and binding sites
- URE · Urea · ligand · 10 copies · chains A, C, B, D
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.74 | 0.92 | 36 | empty |
| 2 | 204 | 0.70 | 0.88 | 41 | URE |
| 3 | 287 | 0.65 | 0.81 | 40 | URE, PYR |
| 4 | 266 | 0.65 | 0.82 | 39 | PYR |
| 5 | 308 | 0.64 | 0.80 | 43 | URE, PYR |
Interfaces
4 interfaces between chains.
- C–D · 1720 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1714 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 990 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 963 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4U4M · Crystal structure of 0.5M urea unfolded YagE, a KDG aldolase protein in complex with… · 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
- Elsewhere: RCSB PDB 4U4M · PDBe 4U4M
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