Research workbench
Crystal structure of prc with S452I and L252Y mutations in complex with nlpi
Analyse Crystal structure of prc with S452I and L252Y mutations 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
- 6IQQ
- Type
- protein
- Length
- 1,802 residues
- Chains
- 4
- 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
- Ligands
- CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein nlpi | protein | 257 | 74% helix, 0% strand | P0AFB1 |
| B | Lipoprotein nlpi | protein | 258 | 74% helix, 0% strand | P0AFB1 |
| C | Tail-specific protease (EC 3.4.21.102) | protein | 645 | 41% helix, 16% strand | P23865 |
| D | Tail-specific protease (EC 3.4.21.102) | protein | 642 | 41% helix, 17% strand | P23865 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains C, D
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 | 835 | 0.86 | 0.88 | 83 | empty |
| 2 | 698 | 0.85 | 0.89 | 71 | empty |
| 3 | 212 | 0.69 | 0.86 | 40 | empty |
| 4 | 147 | 0.63 | 0.86 | 34 | empty |
| 5 | 135 | 0.58 | 0.84 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1289 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1016 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 977 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6IQQ · Crystal structure of Prc with S452I and L252Y mutations in complex with NlpI · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.79
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 6IQQ · PDBe 6IQQ · UniProt P0AFB1 · UniProt P23865
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