MolNFT v1 · #152707 · protein
Crystal structure of prc with L245A and L340G mutations in complex with nlpi
6IQS · Lipoprotein nlpi: “Crystal structure of prc with L245A and L340G mutations in complex with nlpi”. X-ray diffraction, 20 pockets (best druggability 0.59). MolNFT v1 #152707 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6IQS
- Type
- protein
- Length
- 1,594 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
- Pockets
- 20 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein nlpi | protein | 256 | 75% helix, 0% strand | P0AFB1 |
| B | Lipoprotein nlpi | protein | 259 | 74% helix, 0% strand | P0AFB1 |
| C | Tail-specific protease (EC 3.4.21.102) | protein | 541 | 47% helix, 13% strand | P23865 |
| D | Tail-specific protease (EC 3.4.21.102) | protein | 538 | 47% helix, 13% strand | P23865 |
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.59 | 0.83 | 31 | empty |
| 2 | 241 | 0.54 | 0.77 | 28 | empty |
| 3 | 208 | 0.52 | 0.77 | 26 | empty |
| 4 | 255 | 0.49 | 0.74 | 31 | empty |
| 5 | 164 | 0.48 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1368 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1064 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1034 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6IQS · Crystal structure of Prc with L245A and L340G 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 D against A, TM-score 0.93
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 6IQS · PDBe 6IQS · UniProt P0AFB1 · UniProt P23865
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