MolNFT v1 · #61799 · protein
Trypanosoma cruzi metallocarboxypeptidase 1
3DWC: “Trypanosoma cruzi metallocarboxypeptidase 1”. X-ray diffraction, 2 ligands (CO, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #61799 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DWC
- Type
- protein
- Length
- 1,991 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallocarboxypeptidase
- EC
- 3.4.17.19
- UniProt
- Q6ZXC0
- Ligands
- CO, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Metallocarboxypeptidase (EC 3.4.17.19) | protein | 501 | 68% helix, 3% strand | Q6ZXC0 |
| B | Metallocarboxypeptidase (EC 3.4.17.19) | protein | 506 | 67% helix, 3% strand | Q6ZXC0 |
| D | Metallocarboxypeptidase (EC 3.4.17.19) | protein | 483 | 66% helix, 4% strand | Q6ZXC0 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 4 copies · chains A, C, D, B
- SO4 · Sulfate ion · ion · 13 copies · chains A, C, D, B
- GOL · Glycerol · additive · 9 copies · chains A, B, 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 | 1015 | 0.80 | 0.81 | 82 | CO |
| 2 | 926 | 0.79 | 0.81 | 87 | CO |
| 3 | 954 | 0.79 | 0.81 | 83 | CO, SO4 |
| 4 | 1186 | 0.77 | 0.79 | 97 | empty |
| 5 | 1094 | 0.70 | 0.75 | 90 | GOL, SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1475 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1465 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 375 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 3DWC · Trypanosoma Cruzi Metallocarboxypeptidase 1 · 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 Q6ZXC0
- Elsewhere: RCSB PDB 3DWC · PDBe 3DWC · UniProt Q6ZXC0
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