Research workbench
Crystal structure of a T325I/T329I/H333Y/H335Q mutant of thrombin- activatable fibrinolysis inhibitor (tafi-iiyq)
Analyse Crystal structure of a T325I/T329I/H333Y/H335Q mutant of thrombin- activatable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D68
- Type
- protein
- Length
- 1,203 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase B2
- EC
- 3.4.17.20
- UniProt
- Q96IY4
- Ligands
- ARG, NAG, ZN
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Carboxypeptidase B2 (EC 3.4.17.20) | protein | 401 | 42% helix, 18% strand | Q96IY4 |
Ligands and binding sites
- ARG · Arginine · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.78 | 0.81 | 78 | empty |
| 2 | 294 | 0.73 | 0.86 | 36 | ARG |
| 3 | 315 | 0.73 | 0.85 | 37 | ZN, ARG |
| 4 | 297 | 0.73 | 0.86 | 39 | ZN, ARG |
| 5 | 302 | 0.57 | 0.76 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–C · 836 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 587 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 134 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 9 disulfide (N-glycosylation, disulfide).
Compared structures
- 3D68 · Crystal structure of a T325I/T329I/H333Y/H335Q mutant of Thrombin-Activatable… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96IY4 · AlphaFold monomer V2.0 prediction for carboxypeptidase B2 (Q96IY4) · a predicted model of the same protein · chain C 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 Q96IY4
- Elsewhere: RCSB PDB 3D68 · PDBe 3D68 · UniProt Q96IY4
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