MolNFT v1 · #152709 · protein
Crystal structure of prc with PDZ domain deletion in complex with nlpi
6IQU · Lipoprotein nlpi: “Crystal structure of prc with PDZ domain deletion in complex with nlpi”. X-ray diffraction, 8 pockets (best druggability 0.53). MolNFT v1 #152709 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IQU
- Type
- protein
- Length
- 798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein nlpi; Tail-specific protease
- EC
- 3.4.21.102
- UniProt
- P0AFB1, P23865
- Pockets
- 8 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein nlpi | protein | 259 | 70% helix, 0% strand | P0AFB1 |
| B | Tail-specific protease (EC 3.4.21.102) | protein | 539 | 46% helix, 14% strand | P23865 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.53 | 0.77 | 28 | empty |
| 2 | 216 | 0.51 | 0.76 | 29 | empty |
| 3 | 140 | 0.48 | 0.78 | 21 | empty |
| 4 | 206 | 0.46 | 0.74 | 33 | empty |
| 5 | 99 | 0.46 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 982 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6IQU · Crystal structure of Prc with PDZ domain deletion in complex with NlpI · the same entry in another collection · chain A against A, TM-score 1.00
- P0AFB1 · AlphaFold monomer V2.0 prediction for lipoprotein nlpi (P0AFB1) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P23865 · AlphaFold monomer V2.0 prediction for tail-specific protease (P23865) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P0AFB1
- Every structure of UniProt P23865
- Elsewhere: RCSB PDB 6IQU · PDBe 6IQU · UniProt P0AFB1 · UniProt P23865
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