MolNFT v1 · #152705 · protein
Crystal structure of prc with S452I and L252Y mutations in complex with nlpi
6IQQ · Lipoprotein nlpi: “Crystal structure of prc with S452I and L252Y mutations in complex with nlpi”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.86). MolNFT v1 #152705 on GenesisL1: 3D structure, binding sites and…
- 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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