MolNFT v1 · #132972 · protein
Crystal structure of kemp eliminase HG3.14 with bound transition state analogue, 277K
5RGD: “Crystal structure of kemp eliminase HG3.14 with bound transition state analogue, 277K”. X-ray diffraction, 2 ligands (6NT, SO4), 2 pockets (best druggability 0.79). MolNFT v1 #132972 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5RGD
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kemp eliminase HG3.14
- EC
- 3.2.1.8
- UniProt
- P23360
- Ligands
- 6NT, SO4
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kemp eliminase HG3.14 (EC 3.2.1.8) | protein | 300 | 45% helix, 20% strand | P23360 |
Ligands and binding sites
- 6NT · 6-nitrobenzotriazole · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.79 | 0.86 | 58 | 6NT |
| 2 | 186 | 0.64 | 0.84 | 35 | 6NT |
Interfaces
1 interface between chains.
- A–B · 895 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5RGD · Crystal Structure of Kemp Eliminase HG3.14 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 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 P23360
- Elsewhere: RCSB PDB 5RGD · PDBe 5RGD · UniProt P23360
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.