Research workbench
Crystal structure of H177A mutant of glyceraldehyde-3-phosphate- DEHYDROGENASE1 from escherichia COLI complexed with NAD at 1.98 ångström resolution.
Analyse Crystal structure of H177A mutant of glyceraldehyde-3-phosphate- DEHYDROGENASE1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C5O
- Type
- protein
- Length
- 1,339 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- A0A140NCK4
- Ligands
- NAD, CL, PO4
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 338 | 29% helix, 28% strand | A0A140NCK4 |
| P, R | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 334 | 30% helix, 28% strand | A0A140NCK4 |
| Q | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 333 | 30% helix, 28% strand | A0A140NCK4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, R, P, Q
- CL · Chloride ion · ion · 5 copies · chains O, P, Q, R
- PO4 · Phosphate ion · ion · chains O, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.79 | 0.95 | 46 | PO4 |
| 2 | 1133 | 0.77 | 0.79 | 121 | NAD |
| 3 | 624 | 0.72 | 0.80 | 75 | NAD |
| 4 | 448 | 0.69 | 0.80 | 60 | NAD |
| 5 | 435 | 0.60 | 0.75 | 46 | empty |
Interfaces
6 interfaces between chains.
- Q–R · 2019 Ų buried · 45 hydrogen bonds · protein-protein
- O–P · 2011 Ų buried · 47 hydrogen bonds · protein-protein
- P–Q · 1418 Ų buried · 19 hydrogen bonds · protein-protein
- O–R · 1413 Ų buried · 20 hydrogen bonds · protein-protein
- P–R · 585 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7C5O · Crystal Structure of H177A mutant of Glyceraldehyde-3-phosphate-dehydrogenase1 from… · the same entry in another collection · chain O against O, 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 A0A140NCK4
- Elsewhere: RCSB PDB 7C5O · PDBe 7C5O · UniProt A0A140NCK4
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