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Crystal structure of mycobacterium tuberculosis zinc metalloprotease ZMP1 in complex with inhibitor
Analyse Crystal structure of mycobacterium tuberculosis zinc metalloprotease ZMP1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZUK
- Type
- protein
- Length
- 1,314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endopeptidase, peptidase family M13
- EC
- 3.4.24.-
- UniProt
- O53649
- Ligands
- RDF, 211, ZN, CA, SO4, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endopeptidase, peptidase family M13 (EC 3.4.24.-) | protein | 657 | 58% helix, 7% strand | O53649 |
Ligands and binding sites
- RDF · N-alpha-L-rhamnopyranosyloxy(hydroxyphosphinyl)-L-leucyl-L-tryptophan · ligand · 2 copies · chains A, B
- 211 · 2,2',2''-nitrilotriethanol · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 30 copies · chains A, B
- ACT · Acetate ion · additive · 13 copies · chains A, B
- PGE · Triethylene glycol · additive · 8 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.85 | 0.86 | 137 | RDF, PEG, PG4, ACT |
| 2 | 453 | 0.69 | 0.80 | 32 | PEG, ACT |
| 3 | 225 | 0.67 | 0.84 | 27 | PGE |
| 4 | 237 | 0.62 | 0.81 | 26 | empty |
| 5 | 168 | 0.57 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 522 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3ZUK · Crystal structure of mycobacterium tuberculosis zinc metalloprotease ZMP1 in complex with… · 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 O53649
- Elsewhere: RCSB PDB 3ZUK · PDBe 3ZUK · UniProt O53649
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