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Crystal structure of the b' domain of human protein disulfide isomerase-like protein of the testis (PDILT)
Analyse Crystal structure of the b' domain of human protein disulfide isomerase-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NWY
- Type
- protein
- Length
- 493 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens
- Molecule
- Protein disulfide-isomerase-like protein of the testis
- EC
- 5.3.4.1
- UniProt
- Q8N807
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · resolution 2 · 4 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein disulfide-isomerase-like protein of the testis (EC 5.3.4.1) | protein | 128 | 35% helix, 20% strand | Q8N807 |
| B | Protein disulfide-isomerase-like protein of the testis (EC 5.3.4.1) | protein | 118 | 34% helix, 21% strand | Q8N807 |
| C | Protein disulfide-isomerase-like protein of the testis (EC 5.3.4.1) | protein | 124 | 35% helix, 20% strand | Q8N807 |
| D | Protein disulfide-isomerase-like protein of the testis (EC 5.3.4.1) | protein | 123 | 34% helix, 20% strand | Q8N807 |
Ligands and binding sites
- FMT · Formic acid · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.66 | 0.80 | 45 | FMT |
| 2 | 124 | 0.46 | 0.77 | 19 | empty |
| 3 | 105 | 0.42 | 0.76 | 16 | empty |
| 4 | 129 | 0.38 | 0.73 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 759 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 322 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 104 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4NWY · Crystal structure of the B' domain of human protein disulfide isomerase-like protein of… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8N807 · AlphaFold monomer V2.0 prediction for protein disulfide-isomerase- like protein of the… · a predicted model of the same protein · chain D 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 Q8N807
- Elsewhere: RCSB PDB 4NWY · PDBe 4NWY · UniProt Q8N807
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