MolNFT v1 · #103008 · protein
MT1-MMP:FAB complex (form I)
4P3C · Heavy chain Fab fragment of antibody lem-2/15: “MT1-MMP:FAB complex (form I)”. X-ray diffraction, 2 ligands (MG, CL), 4 pockets (best druggability 0.62). MolNFT v1 #103008 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4P3C
- Type
- protein
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain Fab fragment of antibody lem-2/15; Light chain Fab fragment of antibody…
- EC
- 3.4.24.80
- UniProt
- P50281
- Ligands
- MG, CL
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain Fab fragment of antibody lem-2/15 | protein | 218 | 10% helix, 53% strand | — |
| L | Light chain Fab fragment of antibody lem-2/15 | protein | 218 | 6% helix, 54% strand | — |
| M | Matrix metalloproteinase-14 (EC 3.4.24.80) | protein | 13 | 0% helix, 0% strand | P50281 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains L
- CL · Chloride ion · ion · chains H
- EDO · 1,2-ethanediol · additive · 6 copies · chains H, L, M
- ACT · Acetate ion · additive · 3 copies · chains H, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.62 | 0.75 | 61 | EDO |
| 2 | 59 | 0.36 | 0.79 | 18 | EDO |
| 3 | 58 | 0.31 | 0.76 | 13 | empty |
| 4 | 62 | 0.29 | 0.74 | 21 | ACT |
Interfaces
3 interfaces between chains.
- H–L · 1772 Ų buried · 18 hydrogen bonds · protein-protein
- H–M · 570 Ų buried · 9 hydrogen bonds · protein-protein
- L–M · 304 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P50281
- Elsewhere: RCSB PDB 4P3C · PDBe 4P3C · UniProt P50281
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.