MolNFT v1 · #53227 · protein
MMP12 complex with a beta hydroxy carboxylic acid
2WO8 · Macrophage metalloelastase: “MMP12 complex with a beta hydroxy carboxylic acid”. X-ray diffraction, 5 ligands (077, 023, ZN), 8 pockets (best druggability 0.58). MolNFT v1 #53227 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2WO8
- Type
- protein
- Length
- 649 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage metalloelastase
- EC
- 3.4.24.65
- UniProt
- P39900
- Ligands
- 077, 023, ZN, CA, SO4
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Macrophage metalloelastase (EC 3.4.24.65) | protein | 163 | 24% helix, 17% strand | P39900 |
| D | Macrophage metalloelastase (EC 3.4.24.65) | protein | 160 | 26% helix, 17% strand | P39900 |
Ligands and binding sites
- 077 · (3S)-5-biphenyl-4-yl-3-hydroxypentanoic acid · ligand · 2 copies · chains A, C
- 023 · N^2^-[(2R)-2-{(1S)-1-[formyl(hydroxy)amino]ethyl}-5-phenylpentanoyl]-N,3-dimethyl-L-valinamide · ligand · 2 copies · chains B, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, D, B, C
- GOL · Glycerol · additive · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.58 | 0.80 | 27 | 077 |
| 2 | 422 | 0.58 | 0.74 | 39 | empty |
| 3 | 152 | 0.54 | 0.80 | 27 | 077 |
| 4 | 81 | 0.52 | 0.84 | 20 | 023 |
| 5 | 100 | 0.52 | 0.82 | 24 | 023 |
Interfaces
2 interfaces between chains.
- A–B · 196 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 187 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2WO8 · MMP12 complex with a beta hydroxy carboxylic acid · 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 2WO8 · PDBe 2WO8 · UniProt P39900
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