MolNFT v1 · #79437 · protein
Crystal structure of the complex of camel peptidoglycan recognition PROTEIN(CPGRP-S) with a mycobacterium metabolite shikimate at 2.7 a resolution
3T39 · Peptidoglycan recognition protein 1: “Crystal structure of the complex of camel peptidoglycan recognition PROTEIN(CPGRP-S) with a mycobacterium…”. X-ray diffraction, 2 ligands (SRT, SKM), 6 pockets (best druggability 0.82). MolNFT…
- PDB
- 3T39
- 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
- SRT, SKM
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein 1 | protein | 171 | 34% helix, 20% strand | Q9GK12 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · chains C, D
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · chains A, B, D
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.82 | 0.86 | 96 | GOL, SRT |
| 2 | 57 | 0.66 | 0.95 | 23 | empty |
| 3 | 286 | 0.63 | 0.80 | 39 | SKM |
| 4 | 74 | 0.40 | 0.79 | 17 | empty |
| 5 | 61 | 0.32 | 0.76 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 763 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 533 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 356 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 90 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 86 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3T39 · Crystal structure of the complex of camel peptidoglycan recognition protein(CPGRP-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 3T39 · PDBe 3T39 · UniProt Q9GK12
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