Research workbench
A fungal glyceraldehyde-3-phosphate dehydrogenase with self-resistance to inhibitor heptelidic acid
Analyse A fungal glyceraldehyde-3-phosphate dehydrogenase with self-resistance to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M5X
- Type
- protein
- Length
- 1,335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- G9NDK9
- Ligands
- NAD, PO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, R, Q | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 334 | 33% helix, 27% strand | G9NDK9 |
| P | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 333 | 33% helix, 27% strand | G9NDK9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, R, P, Q
- PO4 · Phosphate ion · ion · 5 copies · chains O, R, P, Q
- EDO · 1,2-ethanediol · additive · 25 copies · chains O, P, Q, R
- GOL · Glycerol · additive · 6 copies · chains O, R, P, Q
- PEG · Di(hydroxyethyl)ether · additive · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.77 | 0.79 | 123 | EDO, NAD, PO4, GOL |
| 2 | 1186 | 0.75 | 0.77 | 127 | EDO, NAD, PO4, PEG |
| 3 | 459 | 0.72 | 0.82 | 50 | EDO |
| 4 | 457 | 0.70 | 0.81 | 52 | EDO |
| 5 | 55 | 0.68 | 0.96 | 17 | empty |
Interfaces
6 interfaces between chains.
- R–Q · 1992 Ų buried · 28 hydrogen bonds · protein-protein
- O–P · 1987 Ų buried · 27 hydrogen bonds · protein-protein
- P–Q · 1434 Ų buried · 23 hydrogen bonds · protein-protein
- O–R · 1433 Ų buried · 25 hydrogen bonds · protein-protein
- O–Q · 702 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6M5X · A fungal glyceraldehyde-3-phosphate dehydrogenase with self-resistance to inhibitor… · 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 G9NDK9
- Elsewhere: RCSB PDB 6M5X · PDBe 6M5X · UniProt G9NDK9
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