MolNFT v1 · #6619 · protein
Rat granzyme B [N66Q] complexed to ecotin [81-84 iepd]
1FI8 · Natural killer cell protease 1: “Rat granzyme B [N66Q] complexed to ecotin [81-84 iepd]”. X-ray diffraction, 4 pockets (best druggability 0.79). MolNFT v1 #6619 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1FI8
- Type
- protein
- Length
- 703 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Natural killer cell protease 1; Ecotin
- EC
- 3.4.21.-
- UniProt
- P18291, P23827
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Natural killer cell protease 1 (EC 3.4.21.-) | protein | 226 | 10% helix, 38% strand | P18291 |
| C | Ecotin | protein | 78 | 8% helix, 45% strand | P23827 |
| D, F | Ecotin | protein | 48 | 8% helix, 54% strand | P23827 |
| B | Natural killer cell protease 1 (EC 3.4.21.-) | protein | 227 | 10% helix, 39% strand | P18291 |
| E | Ecotin | protein | 76 | 8% helix, 43% strand | P23827 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.79 | 0.81 | 106 | empty |
| 2 | 263 | 0.52 | 0.76 | 44 | empty |
| 3 | 109 | 0.41 | 0.77 | 23 | empty |
| 4 | 55 | 0.37 | 0.80 | 23 | empty |
Interfaces
14 interfaces between chains.
- C–D · 2275 Ų buried · 57 hydrogen bonds · protein-protein
- E–F · 2264 Ų buried · 56 hydrogen bonds · protein-protein
- D–F · 1007 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 717 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 685 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1FI8 · Rat granzyme B [N66Q] complexed to ecotin [81-84 iepd] · the same entry in another collection · chain F against F, TM-score 1.00
- P18291 · AlphaFold monomer V2.0 prediction for granzyme B (P18291) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P23827 · AlphaFold monomer V2.0 prediction for ecotin (P23827) · a predicted model of the same protein · chain E 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 P18291
- Every structure of UniProt P23827
- Elsewhere: RCSB PDB 1FI8 · PDBe 1FI8 · UniProt P18291 · UniProt P23827
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