Research workbench
Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with Hg2+ from Lactobacillus plantarum
Analyse Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IQV
- Type
- protein
- Length
- 1,335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.13
- Source
- Lactobacillus plantarum subsp. plantarum JCM 1149
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase, type I
- EC
- 1.2.1.12
- UniProt
- D7VA33
- Ligands
- HG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.13 · 4 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate dehydrogenase, type I (EC 1.2.1.12) | protein | 340 | 29% helix, 27% strand | D7VA33 |
| B | Glyceraldehyde-3-phosphate dehydrogenase, type I (EC 1.2.1.12) | protein | 336 | 30% helix, 27% strand | D7VA33 |
| C | Glyceraldehyde-3-phosphate dehydrogenase, type I (EC 1.2.1.12) | protein | 326 | 28% helix, 26% strand | D7VA33 |
| D | Glyceraldehyde-3-phosphate dehydrogenase, type I (EC 1.2.1.12) | protein | 333 | 27% helix, 26% strand | D7VA33 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 11 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, D, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.79 | 0.80 | 113 | TRS |
| 2 | 935 | 0.75 | 0.79 | 121 | HG |
| 3 | 1006 | 0.75 | 0.78 | 119 | HG |
| 4 | 114 | 0.47 | 0.78 | 19 | empty |
| 5 | 99 | 0.42 | 0.78 | 21 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2079 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2078 Ų buried · 50 hydrogen bonds · protein-protein
- B–D · 1374 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1360 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 438 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6IQV · Crystal structure of cell surface glyceraldehyde-3-phosphate dehydrogenase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
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 D7VA33
- Elsewhere: RCSB PDB 6IQV · PDBe 6IQV · UniProt D7VA33
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.