MolNFT v1 · #142563 · protein
Crystal structure of the ternary complex of peptidoglycan recognition protein (pgrp-S) with tartaric acid, ribose and 2,6-diaminopimelic acid at 2.11 a resolution
6A89 · Peptidoglycan recognition protein 1: “Crystal structure of the ternary complex of peptidoglycan recognition protein (pgrp-S) with tartaric acid…”. X-ray diffraction, 2 ligands (API, RIB), 4 pockets (best druggability 0.79). MolNFT…
- PDB
- 6A89
- Type
- protein
- Length
- 668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan recognition protein 1
- UniProt
- Q9GK12
- Ligands
- API, RIB
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein 1 | protein | 167 | 29% helix, 20% strand | Q9GK12 |
Ligands and binding sites
- API · 2,6-diaminopimelic acid · ligand · chains A, B, D
- RIB · alpha-D-ribofuranose · ligand · chains A, D
- EDO · 1,2-ethanediol · additive · chains A
- GOL · Glycerol · additive · chains C, D
- TLA · L(+)-tartaric acid · additive · chains C, D
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 | 1129 | 0.79 | 0.80 | 123 | EDO, GOL, TLA, RIB |
| 2 | 55 | 0.67 | 0.96 | 22 | empty |
| 3 | 67 | 0.27 | 0.72 | 21 | empty |
| 4 | 55 | 0.26 | 0.73 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 687 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 543 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 347 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 71 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6A89 · Crystal structure of the ternary complex of peptidoglycan recognition protein (PGRP-S)… · 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 0.99
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 6A89 · PDBe 6A89 · UniProt Q9GK12
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