Research workbench
Crystal structure of the catalytic domain of mmp-16/MT3-mmp: characterization of mt-mmp specific features
Analyse Crystal structure of the catalytic domain of mmp-16/MT3-mmp: characterization… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RM8
- Type
- protein
- Length
- 169 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metalloproteinase-16
- EC
- 3.4.24.-
- UniProt
- P51512
- Ligands
- BAT, ZN, CA
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix metalloproteinase-16 (EC 3.4.24.-) | protein | 169 | 24% helix, 16% strand | P51512 |
Ligands and binding sites
- BAT · 4-(N-hydroxyamino)-2R-isobutyl-2S-(2-thienylthiomethyl)succinyl-L-phenylalanine-N-methylamide · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.50 | 0.83 | 20 | ZN, BAT |
| 2 | 95 | 0.40 | 0.77 | 14 | empty |
Compared structures
- 1RM8 · Crystal structure of the catalytic domain of MMP-16/MT3-MMP: Characterization of MT-MMP… · the same entry in another collection · chain A against A, TM-score 1.00
- P51512 · AlphaFold monomer V2.0 prediction for matrix metalloproteinase-16 (P51512) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P51512
- Elsewhere: RCSB PDB 1RM8 · PDBe 1RM8 · UniProt P51512
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