Research workbench
Crystal structure of the complex of peptidoglycan recognition protein- short (cpgrp-S) with mycolic acid at 2.5 a resolution
Analyse Crystal structure of the complex of peptidoglycan recognition protein- short… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T2V
- 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
- KKJ
- Pockets
- 5 · best druggability 0.81
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
- KKJ · (2S,3R)-2-hexyl-3-hydroxynonanoic acid · ligand · chains A, B, 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.81 | 0.83 | 126 | TLA, GOL, KKJ |
| 2 | 96 | 0.33 | 0.73 | 27 | empty |
| 3 | 57 | 0.32 | 0.76 | 14 | empty |
| 4 | 56 | 0.30 | 0.75 | 12 | empty |
| 5 | 56 | 0.27 | 0.74 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 786 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 530 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 328 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 107 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 71 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3T2V · Crystal structure of the complex of peptidoglycan recognition protein-short (CPGRP-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 0.97
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 3T2V · PDBe 3T2V · UniProt Q9GK12
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