MolNFT v1 · #117174 · protein
Crystal structure of the complex of peptidoglycan recognition protein pgrp-S with N-acetyl muramic acid at 2.6 a resolution
5E0B · Peptidoglycan recognition protein 1: “Crystal structure of the complex of peptidoglycan recognition protein pgrp-S with N-acetyl muramic acid at…”. X-ray diffraction, 1 ligand (AMU), 4 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5E0B
- 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
- AMU
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein 1 | protein | 171 | 33% helix, 20% strand | Q9GK12 |
Ligands and binding sites
- AMU · N-acetyl-beta-muramic acid · ligand · chains A, C, D
- TLA · L(+)-tartaric acid · additive · chains C, D
- GOL · Glycerol · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.83 | 0.84 | 133 | TLA, AMU, GOL |
| 2 | 112 | 0.35 | 0.73 | 20 | empty |
| 3 | 65 | 0.28 | 0.73 | 19 | empty |
| 4 | 54 | 0.26 | 0.73 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 834 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 526 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 131 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 82 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5E0B · Crystal structure of the complex of Peptidoglycan recognition protein PGRP-S 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 5E0B · PDBe 5E0B · UniProt Q9GK12
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