MolNFT v1 · #91787 · protein
Crystal structure of the complex of cpgrp-S with stearic acid at 2.2 a resolution
4FNN · Peptidoglycan recognition protein 1: “Crystal structure of the complex of cpgrp-S with stearic acid at 2.2 a resolution”. X-ray diffraction, 1 ligand (STE), 3 pockets (best druggability 0.81). MolNFT v1 #91787 on GenesisL1: 3D…
- PDB
- 4FNN
- Type
- protein
- Length
- 684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan recognition protein 1
- UniProt
- Q9GK12
- Ligands
- STE
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein 1 | protein | 171 | 30% helix, 19% strand | Q9GK12 |
Ligands and binding sites
- STE · Stearic acid · ligand · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.81 | 0.83 | 142 | STE |
| 2 | 203 | 0.61 | 0.82 | 42 | empty |
| 3 | 53 | 0.25 | 0.73 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 893 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 526 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 344 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 118 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 70 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4FNN · Crystal structure of the complex of CPGRP-S with stearic acid at 2.2 A RESOLUTION · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GK12 · AlphaFold monomer V2.0 prediction for peptidoglycan recognition protein 1 (Q9GK12) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9GK12
- Elsewhere: RCSB PDB 4FNN · PDBe 4FNN · UniProt Q9GK12
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