Research workbench
X-ray crystal structure of soybean trypsin inhibitor (kunitz) complexed with 1,5-disulfonyl naphthalene
Analyse X-ray crystal structure of soybean trypsin inhibitor (kunitz) complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NTT
- Type
- protein
- Length
- 351 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypsin inhibitor a
- UniProt
- P01070
- Ligands
- 21D
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trypsin inhibitor a | protein | 175 | 2% helix, 43% strand | P01070 |
| B | Trypsin inhibitor a | protein | 176 | 2% helix, 40% strand | P01070 |
Ligands and binding sites
- 21D · naphthalene-1,5-disulfonic acid · ligand · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.68 | 0.74 | 53 | 21D |
| 2 | 98 | 0.42 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 253 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6NTT · X-ray Crystal Structure of Soybean Trypsin Inhibitor (Kunitz) Complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P01070 · AlphaFold monomer V2.0 prediction for trypsin inhibitor a (P01070) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P01070
- Elsewhere: RCSB PDB 6NTT · PDBe 6NTT · UniProt P01070
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