MolNFT v1 · #103009 · protein
MT1-MMP:FAB complex (form II)
4P3D · Heavy chain Fab fragment of antibody lem-2/15: “MT1-MMP:FAB complex (form II)”. X-ray diffraction, 2 ligands (MG, CL), 5 pockets (best druggability 0.80). MolNFT v1 #103009 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4P3D
- Type
- protein
- Length
- 898 residues
- Chains
- 6
- 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
- A2NHM3, P50281
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Heavy chain Fab fragment of antibody lem-2/15 | protein | 218 | 8% helix, 53% strand | — |
| B, L | Light chain Fab fragment of antibody lem-2/15 | protein | 218 | 6% helix, 52% strand | A2NHM3 |
| C, 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 · 2 copies · chains A, H
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, H, M
- GOL · Glycerol · additive · 2 copies · chains A, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.80 | 0.81 | 120 | empty |
| 2 | 1094 | 0.80 | 0.81 | 113 | empty |
| 3 | 277 | 0.58 | 0.78 | 47 | GOL |
| 4 | 76 | 0.45 | 0.81 | 18 | empty |
| 5 | 62 | 0.30 | 0.74 | 16 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1759 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1731 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 984 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 575 Ų buried · 9 hydrogen bonds · protein-protein
- H–M · 571 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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 A2NHM3
- Every structure of UniProt P50281
- Elsewhere: RCSB PDB 4P3D · PDBe 4P3D · UniProt A2NHM3 · UniProt P50281
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