MolNFT v1 · #174951 · protein
Structure of human neutrophil elastase ecotin complex
7CBK: “Structure of human neutrophil elastase ecotin complex”. X-ray diffraction, 4 ligands (NAG, FUC, MG), 10 pockets (best druggability 0.82). MolNFT v1 #174951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7CBK
- Type
- protein
- Length
- 700 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ecotin; Neutrophil elastase
- EC
- 3.4.21.37
- UniProt
- P23827, P08246
- Ligands
- NAG, FUC, MG, SO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ecotin | protein | 132 | 5% helix, 56% strand | P23827 |
| D, B | Neutrophil elastase (EC 3.4.21.37) | protein | 218 | 8% helix, 39% strand | P08246 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains D, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains D, B
- MG · Magnesium ion · metal · chains D
- SO4 · Sulfate ion · ion · 2 copies · chains D, B
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.82 | 0.83 | 118 | empty |
| 2 | 61 | 0.53 | 0.88 | 18 | empty |
| 3 | 268 | 0.53 | 0.75 | 52 | empty |
| 4 | 191 | 0.53 | 0.78 | 23 | empty |
| 5 | 84 | 0.42 | 0.79 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1486 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 750 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 748 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 440 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 436 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7CBK · Structure of Human Neutrophil Elastase Ecotin complex · the same entry in another collection · chain B against B, TM-score 1.00
- P08246 · AlphaFold monomer V2.0 prediction for neutrophil elastase (P08246) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P23827 · AlphaFold monomer V2.0 prediction for ecotin (P23827) · a predicted model of the same protein · chain A 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 P23827
- Every structure of UniProt P08246
- Elsewhere: RCSB PDB 7CBK · PDBe 7CBK · UniProt P23827 · UniProt P08246
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