Research workbench
Crystal structure of prc with PDZ domain deletion in complex with nlpi
Analyse Crystal structure of prc with PDZ domain deletion in complex with nlpi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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