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Crystal structure of kemp eliminase hg-2 complexed with transition state analog 5-nitro benzotriazole
Analyse Crystal structure of kemp eliminase hg-2 complexed with transition state analog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NYD
- Type
- protein
- Length
- 603 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
- 3NY, SO4
- Pockets
- 3 · best druggability 0.80
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 | 303 | 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
- 3NY · 5-nitro-1H-benzotriazole · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 4 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 | 291 | 0.80 | 0.92 | 29 | empty |
| 2 | 150 | 0.65 | 0.87 | 38 | 3NY |
| 3 | 88 | 0.52 | 0.84 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 940 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3NYD · Crystal Structure of Kemp Eliminase HG-2 Complexed with Transition State Analog 5-Nitro… · 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 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 3NYD · PDBe 3NYD · UniProt P23360
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