MolNFT v1 · #81168 · protein
Crystal structure of the complex of pgrp-S with lauric acid at 2.2 a resolution
3UIL · Peptidoglycan recognition protein 1: “Crystal structure of the complex of pgrp-S with lauric acid at 2.2 a resolution”. X-ray diffraction, 1 ligand (DAO), 4 pockets (best druggability 0.83). MolNFT v1 #81168 on GenesisL1: 3D…
- PDB
- 3UIL
- 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
- DAO
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein 1 | protein | 171 | 31% helix, 19% strand | Q9GK12 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.83 | 0.85 | 112 | GOL |
| 2 | 54 | 0.67 | 0.96 | 23 | empty |
| 3 | 90 | 0.32 | 0.73 | 19 | empty |
| 4 | 66 | 0.27 | 0.72 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 794 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 519 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 341 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 97 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 68 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3UIL · Crystal Structure of the complex of PGRP-S with lauric 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 3UIL · PDBe 3UIL · UniProt Q9GK12
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