MolNFT v1 · #60625 · protein
Crystal structure of the complex of peptidoglycan recognition protein with alpha-D-glucopyranosyl alpha-D-glucopyranoside at 3.4 a resolution
3CXA: “Crystal structure of the complex of peptidoglycan recognition protein with alpha-D-glucopyranosyl…”. X-ray diffraction, 1 ligand (GLC), 2 pockets (best druggability 0.80). MolNFT v1 #60625 on GenesisL1: 3D structure, binding sites…
- PDB
- 3CXA
- Type
- protein
- Length
- 684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan recognition protein
- UniProt
- Q9GK12
- Ligands
- GLC
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein | protein | 171 | 26% helix, 20% strand | Q9GK12 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.80 | 0.83 | 91 | TLA |
| 2 | 918 | 0.73 | 0.77 | 71 | empty |
Interfaces
5 interfaces between chains.
- A–B · 803 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 555 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 365 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 84 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 81 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3CXA · Crystal structure of the complex of peptidoglycan recognition protein with… · 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 0.97
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 3CXA · PDBe 3CXA · UniProt Q9GK12
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