MolNFT v1 · #116094 · protein
Crystal structure of a double mutant catalytic domain of human MMP12 in complex with an hydroxamate analogue of RXP470
5D3C · Macrophage metalloelastase: “Crystal structure of a double mutant catalytic domain of human MMP12 in complex with an hydroxamate analogue…”. X-ray diffraction, 3 ligands (56O, CA, ZN), 2 pockets (best druggability 0.55). MolNFT v1…
- PDB
- 5D3C
- Type
- protein
- Length
- 159 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage metalloelastase
- EC
- 3.4.24.65
- UniProt
- P39900
- Ligands
- 56O, CA, ZN
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrophage metalloelastase (EC 3.4.24.65) | protein | 159 | 26% helix, 17% strand | P39900 |
Ligands and binding sites
- 56O · N-[(2R)-2-{[3-(3'-chlorobiphenyl-4-yl)-1,2-oxazol-5-yl]methyl}-4-(hydroxyamino)-4-oxobutanoyl]-L-alpha-glutamyl-L-alpha-glutamine · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- ZN · Zinc 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.55 | 0.81 | 29 | 56O |
| 2 | 98 | 0.39 | 0.76 | 19 | empty |
Compared structures
- 5D3C · Crystal structure of a double mutant catalytic domain of Human MMP12 in complex with an… · 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 P39900
- Elsewhere: RCSB PDB 5D3C · PDBe 5D3C · UniProt P39900
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