MolNFT v1 · #134848 · protein
Structure determination of a potent, selective antibody inhibitor of human MMP9 (apo MMP9)
5TH6 · Matrix metalloproteinase-9,MATRIX metalloproteinase-9: “Structure determination of a potent, selective antibody inhibitor of human MMP9 (apo MMP9)”. X-ray diffraction, 2 ligands (CA, ZN), 11 pockets (best druggability 0.71). MolNFT…
- PDB
- 5TH6
- Type
- protein
- Length
- 869 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metalloproteinase-9,MATRIX metalloproteinase-9
- EC
- 3.4.24.35
- UniProt
- P14780
- Ligands
- CA, ZN
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix metalloproteinase-9,MATRIX metalloproteinase-9 (EC 3.4.24.35) | protein | 220 | 33% helix, 14% strand | P14780 |
| B | Matrix metalloproteinase-9,MATRIX metalloproteinase-9 (EC 3.4.24.35) | protein | 211 | 33% helix, 14% strand | P14780 |
| C | Matrix metalloproteinase-9,MATRIX metalloproteinase-9 (EC 3.4.24.35) | protein | 221 | 33% helix, 14% strand | P14780 |
| D | Matrix metalloproteinase-9,MATRIX metalloproteinase-9 (EC 3.4.24.35) | protein | 217 | 33% helix, 14% strand | P14780 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.71 | 0.96 | 19 | empty |
| 2 | 81 | 0.70 | 0.94 | 20 | empty |
| 3 | 90 | 0.65 | 0.91 | 24 | empty |
| 4 | 272 | 0.65 | 0.81 | 36 | empty |
| 5 | 268 | 0.62 | 0.80 | 40 | empty |
Interfaces
3 interfaces between chains.
- C–D · 636 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 632 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 230 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5TH6 · Structure determination of a potent, selective antibody inhibitor of human MMP9 (apo MMP9) · the same entry in another collection · chain D against D, TM-score 1.00
- P14780 · AlphaFold monomer V2.0 prediction for matrix metalloproteinase-9 (P14780) · a predicted model of the same protein · chain D 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 P14780
- Elsewhere: RCSB PDB 5TH6 · PDBe 5TH6 · UniProt P14780
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