MolNFT v1 · #114211 · protein
Crystal structure of the catalytic domain of mmp-13 complexed with N- phenyl-4-((4H-1,2,4-triazol-3-YLSULFANYL)METHYL)-1,3-thiazol-2-amine
5B5O · Collagenase 3: “Crystal structure of the catalytic domain of mmp-13 complexed with N…”. X-ray diffraction, 4 ligands (WMM, ZN, CA), 2 pockets (best druggability 0.71). MolNFT v1 #114211 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5B5O
- Type
- protein
- Length
- 332 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
- WMM, ZN, CA, NA
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase 3 (EC 3.4.24.-) | protein | 167 | 24% helix, 19% strand | P45452 |
| B | Collagenase 3 (EC 3.4.24.-) | protein | 165 | 24% helix, 18% strand | P45452 |
Ligands and binding sites
- WMM · N-phenyl-4-[(4H-1,2,4-triazol-3-ylsulfanyl)methyl]-1,3-thiazol-2-amine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 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 | 947 | 0.71 | 0.75 | 97 | EDO, ZN, WMM |
| 2 | 164 | 0.53 | 0.79 | 25 | WMM |
Interfaces
1 interface between chains.
- A–B · 1257 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5B5O · Crystal structure of the catalytic domain of MMP-13 complexed with… · 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 5B5O · PDBe 5B5O · UniProt P45452
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.