MolNFT v1 · #122397 · protein
A C69-family cysteine dipeptidase in complex with met and ala from lactobacillus farciminis
5INX: “A C69-family cysteine dipeptidase in complex with met and ala from lactobacillus farciminis”. X-ray diffraction, 2 ligands (MET, ALA), 20 pockets (best druggability 0.83). MolNFT v1 #122397 on GenesisL1: 3D structure, binding sites…
- PDB
- 5INX
- Type
- protein
- Length
- 2,305 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidase
- UniProt
- A0A0R1IQH8
- Ligands
- MET, ALA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Dipeptidase | protein | 461 | 34% helix, 20% strand | A0A0R1IQH8 |
Ligands and binding sites
- MET · Methionine · ligand · 5 copies · chains A, B, C, D, E
- ALA · Alanine · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.83 | 0.84 | 80 | MET, ALA |
| 2 | 970 | 0.82 | 0.84 | 93 | MET, ALA |
| 3 | 1198 | 0.81 | 0.82 | 96 | MET, ALA |
| 4 | 1170 | 0.81 | 0.82 | 95 | MET, ALA |
| 5 | 1184 | 0.80 | 0.82 | 108 | MET, ALA |
Interfaces
5 interfaces between chains.
- A–E · 880 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 873 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 871 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 871 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 864 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5INX · A C69-family cysteine dipeptidase in complex with Met and Ala from Lactobacillus… · the same entry in another collection · chain B against B, 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 A0A0R1IQH8
- Elsewhere: RCSB PDB 5INX · PDBe 5INX · UniProt A0A0R1IQH8
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