MolNFT v1 · #179413 · protein
Crystal structure of kemp eliminase HG3 in complex with the transition state analog 6-nitrobenzotriazole
7K4Q · Endo-1,4-beta-xylanase: “Crystal structure of kemp eliminase HG3 in complex with the transition state analog 6-nitrobenzotriazole”. X-ray diffraction, 2 ligands (6NT, SO4), 3 pockets (best druggability 0.64). MolNFT v1 #179413 on…
- PDB
- 7K4Q
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- UniProt
- P23360
- Ligands
- 6NT, SO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 297 | 43% helix, 20% strand | P23360 |
| B | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 300 | 44% helix, 19% 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.64 | 0.93 | 17 | 6NT |
| 2 | 147 | 0.43 | 0.75 | 23 | empty |
| 3 | 57 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 289 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7K4Q · Crystal structure of Kemp Eliminase HG3 in complex with the transition state analog… · 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 B 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 7K4Q · PDBe 7K4Q · UniProt P23360
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