MolNFT v1 · #134850 · protein
Structure determination of a potent, selective antibody inhibitor of human MMP9 (gs-5745 bound to mmp-9)
5TH9 · Gs-5745 Fab light chain: “Structure determination of a potent, selective antibody inhibitor of human MMP9 (gs-5745 bound to mmp-9)”. X-ray diffraction, 3 ligands (NCO, ZN, CA), 20 pockets (best druggability 0.78). MolNFT v1 #134850…
- PDB
- 5TH9
- Type
- protein
- Length
- 1,717 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gs-5745 Fab light chain; Gs-5745 Fab heavy chain; Matrix metalloproteinase-9,MATRIX…
- EC
- 3.4.24.35
- UniProt
- P14780
- Ligands
- NCO, ZN, CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Gs-5745 Fab light chain | protein | 214 | 6% helix, 51% strand | — |
| H, I | Gs-5745 Fab heavy chain | protein | 208 | 6% helix, 53% strand | — |
| A, B | Matrix metalloproteinase-9,MATRIX metalloproteinase-9 (EC 3.4.24.35) | protein | 222 | 32% helix, 15% strand | P14780 |
| N | Gs-5745 Fab light chain | protein | 106 | 3% helix, 44% strand | — |
| J | Gs-5745 Fab heavy chain | protein | 106 | 0% helix, 32% strand | — |
| C | Matrix metalloproteinase-9,MATRIX metalloproteinase-9 (EC 3.4.24.35) | protein | 217 | 27% helix, 14% strand | P14780 |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- CA · Calcium ion · metal · 6 copies · chains H, A, I, B, J, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.78 | 0.80 | 89 | empty |
| 2 | 64 | 0.72 | 0.98 | 19 | empty |
| 3 | 64 | 0.71 | 0.97 | 18 | empty |
| 4 | 350 | 0.71 | 0.83 | 35 | empty |
| 5 | 52 | 0.67 | 0.96 | 19 | empty |
Interfaces
14 interfaces between chains.
- L–H · 1673 Ų buried · 9 hydrogen bonds · protein-protein
- M–I · 1658 Ų buried · 12 hydrogen bonds · protein-protein
- N–J · 784 Ų buried · 10 hydrogen bonds · protein-protein
- J–C · 723 Ų buried · 12 hydrogen bonds · protein-protein
- H–A · 689 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5TH9 · Structure determination of a potent, selective antibody inhibitor of human MMP9 (GS-5745… · the same entry in another collection · chain C against C, TM-score 1.00
- P14780 · AlphaFold monomer V2.0 prediction for matrix metalloproteinase-9 (P14780) · 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 P14780
- Elsewhere: RCSB PDB 5TH9 · PDBe 5TH9 · UniProt P14780
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