MolNFT v1 · #70148 · protein
Crystal structure of thioacyl-glyceraldehyde-3-phosphate dehydrogenase 1(GAPDH 1) from methicillin resistant staphylococcus aureus MRSA252
3LC2: “Crystal structure of thioacyl-glyceraldehyde-3-phosphate dehydrogenase 1(GAPDH 1) from methicillin resistant…”. X-ray diffraction, 2 ligands (G3H, CL), 11 pockets (best druggability 0.77). MolNFT v1 #70148 on GenesisL1: 3D…
- PDB
- 3LC2
- Type
- protein
- Length
- 1,336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase 1
- EC
- 1.2.1.12
- UniProt
- Q6GIL8
- Ligands
- G3H, CL
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, Q, R, P | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 334 | 28% helix, 29% strand | Q6GIL8 |
Ligands and binding sites
- G3H · Glyceraldehyde-3-phosphate · ligand · 4 copies · chains O, Q, R, P
- CL · Chloride ion · ion · 3 copies · chains O, Q, R
- GOL · Glycerol · additive · 3 copies · chains O, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.77 | 0.79 | 102 | G3H, CL, GOL |
| 2 | 465 | 0.71 | 0.82 | 51 | G3H, CL, GOL |
| 3 | 429 | 0.70 | 0.82 | 51 | G3H, CL, GOL |
| 4 | 480 | 0.69 | 0.80 | 66 | empty |
| 5 | 447 | 0.63 | 0.77 | 62 | empty |
Interfaces
6 interfaces between chains.
- Q–R · 2192 Ų buried · 49 hydrogen bonds · protein-protein
- O–P · 2177 Ų buried · 53 hydrogen bonds · protein-protein
- O–R · 1481 Ų buried · 27 hydrogen bonds · protein-protein
- Q–P · 1427 Ų buried · 25 hydrogen bonds · protein-protein
- O–Q · 642 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3LC2 · Crystal Structure of Thioacyl-Glyceraldehyde-3-phosphate dehydrogenase 1(GAPDH 1) from… · the same entry in another collection · chain P against P, TM-score 1.00
- Q6GIL8 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase 1 (Q6GIL8) · a predicted model of the same protein · chain R 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 Q6GIL8
- Elsewhere: RCSB PDB 3LC2 · PDBe 3LC2 · UniProt Q6GIL8
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