MolNFT v1 · #85005 · protein
Crystal structure of collagenase-3 (mmp-13) complexed to a diphenyl- ether sulphone based hydroxamic acid
456C: “Crystal structure of collagenase-3 (mmp-13) complexed to a diphenyl- ether sulphone based hydroxamic acid”. X-ray diffraction, 3 ligands (CBP, ZN, CA), 2 pockets (best druggability 0.64). MolNFT v1 #85005 on GenesisL1: 3D structure…
- PDB
- 456C
- Type
- protein
- Length
- 319 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mmp-13
- EC
- 3.4.24.-
- UniProt
- P45452
- Ligands
- CBP, ZN, CA
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mmp-13 (EC 3.4.24.-) | protein | 160 | 25% helix, 18% strand | P45452 |
| B | Mmp-13 (EC 3.4.24.-) | protein | 159 | 25% helix, 17% strand | P45452 |
Ligands and binding sites
- CBP · 2-{4-[4-(4-chloro-phenoxy)-benzenesulfonyl]-tetrahydro-pyran-4-yl}-N-hydroxy-acetamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
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 | 526 | 0.64 | 0.76 | 79 | CBP |
| 2 | 168 | 0.56 | 0.80 | 30 | CBP |
Interfaces
1 interface between chains.
- A–B · 273 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 456C · Crystal structure of collagenase-3 (mmp-13) complexed to a diphenyl-ether sulphone based… · 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 456C · PDBe 456C · UniProt P45452
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