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Crystal structure of the catalytic domain of human matrix metalloproteinase 10
Analyse Crystal structure of the catalytic domain of human matrix metalloproteinase 10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q3A
- Type
- protein
- Length
- 471 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stromelysin-2
- EC
- 3.4.24.22
- UniProt
- P09238
- Ligands
- NGH, CA, ZN
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stromelysin-2 (EC 3.4.24.22) | protein | 156 | 26% helix, 18% strand | P09238 |
| B | Stromelysin-2 (EC 3.4.24.22) | protein | 160 | 25% helix, 17% strand | P09238 |
| C | Stromelysin-2 (EC 3.4.24.22) | protein | 155 | 25% helix, 17% strand | P09238 |
Ligands and binding sites
- NGH · N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 9 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.84 | 0.84 | 118 | NGH |
| 2 | 151 | 0.56 | 0.82 | 26 | empty |
| 3 | 59 | 0.37 | 0.79 | 22 | empty |
| 4 | 81 | 0.32 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 647 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 511 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 284 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1Q3A · Crystal structure of the catalytic domain of human matrix metalloproteinase 10 · the same entry in another collection · chain A against A, TM-score 1.00
- P09238 · AlphaFold monomer V2.0 prediction for stromelysin-2 (P09238) · 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 P09238
- Elsewhere: RCSB PDB 1Q3A · PDBe 1Q3A · UniProt P09238
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