MolNFT v1 · #104781 · protein
X-ray structure of the catalytic domain of mmp-8 with the inhibitor ML115
4QKZ · Neutrophil collagenase: “X-ray structure of the catalytic domain of mmp-8 with the inhibitor ML115”. X-ray diffraction, 3 ligands (QZK, CA, ZN), 1 pocket (best druggability 0.47). MolNFT v1 #104781 on GenesisL1: 3D structure…
- PDB
- 4QKZ
- Type
- protein
- Length
- 163 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil collagenase
- EC
- 3.4.24.34
- UniProt
- P22894
- Ligands
- QZK, CA, ZN
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil collagenase (EC 3.4.24.34) | protein | 163 | 25% helix, 15% strand | P22894 |
Ligands and binding sites
- QZK · {[(biphenyl-4-ylsulfonyl)amino]methanediyl}bis(phosphonic acid) · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.47 | 0.81 | 20 | ZN, QZK |
Compared structures
- 4QKZ · X-ray structure of the catalytic domain of MMP-8 with the inhibitor ML115 · the same entry in another collection · chain A against A, TM-score 1.00
- P22894 · AlphaFold monomer V2.0 prediction for neutrophil collagenase (P22894) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P22894
- Elsewhere: RCSB PDB 4QKZ · PDBe 4QKZ · UniProt P22894
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