MolNFT v1 · #69048 · protein
Crystal structure of human mmp-13 complexed with a phenyl-2H-tetrazole compound
3KEC · Collagenase 3: “Crystal structure of human mmp-13 complexed with a phenyl-2H-tetrazole compound”. X-ray diffraction, 5 ligands (3KE, HAE, CA), 2 pockets (best druggability 0.73). MolNFT v1 #69048 on GenesisL1: 3D structure, binding…
- PDB
- 3KEC
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase 3
- EC
- 3.4.24.-
- UniProt
- P45452
- Ligands
- 3KE, HAE, CA, ZN, SO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Collagenase 3 (EC 3.4.24.-) | protein | 167 | 24% helix, 18% strand | P45452 |
Ligands and binding sites
- 3KE · 4-{[({3-[2-(4-methoxybenzyl)-2H-tetrazol-5-yl]phenyl}carbonyl)amino]methyl}benzoic acid · ligand · 2 copies · chains A, B
- HAE · Acetohydroxamic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.73 | 0.76 | 80 | 3KE, HAE |
| 2 | 288 | 0.61 | 0.79 | 39 | ZN, 3KE, HAE |
Interfaces
1 interface between chains.
- A–B · 1191 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3KEC · Crystal Structure of Human MMP-13 complexed with a phenyl-2H-tetrazole compound · the same entry in another collection · chain A against A, TM-score 1.00
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 P45452
- Elsewhere: RCSB PDB 3KEC · PDBe 3KEC · UniProt P45452
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