Research workbench
Crystal structure of the triticum aestivum xylanase inhibitor-iia in complex with bacillus subtilis xylanase
Analyse Crystal structure of the triticum aestivum xylanase inhibitor-iia in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HD8
- Type
- protein
- Length
- 1,106 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylanase inhibitor; Endo-1,4-beta-xylanase a
- EC
- 3.2.1.8
- UniProt
- Q53IQ4, P18429
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylanase inhibitor | protein | 370 | 14% helix, 37% strand | Q53IQ4 |
| B, D | Endo-1,4-beta-xylanase a (EC 3.2.1.8) | protein | 184 | 5% helix, 66% strand | P18429 |
| C | Xylanase inhibitor | protein | 368 | 14% helix, 38% strand | Q53IQ4 |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.82 | 0.84 | 123 | empty |
| 2 | 277 | 0.60 | 0.79 | 49 | empty |
| 3 | 265 | 0.60 | 0.79 | 43 | empty |
| 4 | 156 | 0.56 | 0.81 | 27 | empty |
| 5 | 197 | 0.54 | 0.79 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1350 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1349 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 314 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 305 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 120 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3HD8 · Crystal structure of the Triticum aestivum xylanase inhibitor-IIA in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P18429 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase a (P18429) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q53IQ4
- Every structure of UniProt P18429
- Elsewhere: RCSB PDB 3HD8 · PDBe 3HD8 · UniProt Q53IQ4 · UniProt P18429
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