MolNFT v1 · #132970 · protein
Crystal structure of kemp eliminase HG3.3B with bound transition state analogue, 277K
5RGB: “Crystal structure of kemp eliminase HG3.3B with bound transition state analogue, 277K”. X-ray diffraction, 2 ligands (6NT, SO4), 3 pockets (best druggability 0.78). MolNFT v1 #132970 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5RGB
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kemp eliminase HG3.3B
- EC
- 3.2.1.8
- UniProt
- P23360
- Ligands
- 6NT, SO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kemp eliminase HG3.3B (EC 3.2.1.8) | protein | 299 | 43% helix, 19% strand | P23360 |
Ligands and binding sites
- 6NT · 6-nitrobenzotriazole · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 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 | 325 | 0.78 | 0.90 | 33 | empty |
| 2 | 236 | 0.69 | 0.85 | 39 | 6NT |
| 3 | 250 | 0.65 | 0.82 | 38 | 6NT |
Interfaces
1 interface between chains.
- A–B · 938 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5RGB · Crystal Structure of Kemp Eliminase HG3.3b 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 5RGB · PDBe 5RGB · UniProt P23360
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.