Research workbench
Crystal structure of kemp eliminase HG4 with bound transition state analogue, 277K
Analyse Crystal structure of kemp eliminase HG4 with bound transition state analogue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5RGF
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kemp eliminase HG3
- EC
- 3.2.1.8
- UniProt
- P23360
- Ligands
- 6NT, SO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kemp eliminase HG3 (EC 3.2.1.8) | protein | 301 | 45% helix, 20% strand | P23360 |
Ligands and binding sites
- 6NT · 6-nitrobenzotriazole · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.77 | 0.87 | 43 | empty |
| 2 | 225 | 0.67 | 0.84 | 40 | 6NT |
| 3 | 218 | 0.63 | 0.82 | 33 | 6NT |
Interfaces
1 interface between chains.
- A–B · 881 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5RGF · Crystal Structure of Kemp Eliminase HG4 with bound transition state analogue, 277K · the same entry in another collection · chain A against A, TM-score 1.00
- P23360 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase (P23360) · a predicted model of the same protein · 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 P23360
- Elsewhere: RCSB PDB 5RGF · PDBe 5RGF · UniProt P23360
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