Research workbench
Crystal structure of the photosynthetic A2B2-glyceraldehyde-3- phosphate dehydrogenase, complexed with NADP
Analyse Crystal structure of the photosynthetic A2B2-glyceraldehyde-3- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PKQ
- Type
- protein
- Length
- 2,052 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase B; Glyceraldehyde-3-phosphate dehydrogenase a
- EC
- 1.2.1.13
- UniProt
- P12860, P19866
- Ligands
- NDP, SO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | Glyceraldehyde-3-phosphate dehydrogenase B (EC 1.2.1.13) | protein | 346 | 27% helix, 23% strand | P12860 |
| P, R | Glyceraldehyde-3-phosphate dehydrogenase a (EC 1.2.1.13) | protein | 337 | 28% helix, 26% strand | P19866 |
| Q | Glyceraldehyde-3-phosphate dehydrogenase B (EC 1.2.1.13) | protein | 347 | 26% helix, 23% strand | P12860 |
| S | Glyceraldehyde-3-phosphate dehydrogenase a (EC 1.2.1.13) | protein | 336 | 29% helix, 26% strand | P19866 |
| T | Glyceraldehyde-3-phosphate dehydrogenase B (EC 1.2.1.13) | protein | 349 | 27% helix, 23% strand | P12860 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains O, R, P, Q, S, T
- SO4 · Sulfate ion · ion · 15 copies · chains O, P, Q, R, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.81 | 0.82 | 82 | empty |
| 2 | 1099 | 0.79 | 0.81 | 105 | SO4, NDP |
| 3 | 1171 | 0.79 | 0.81 | 111 | SO4, NDP |
| 4 | 756 | 0.70 | 0.77 | 71 | SO4, NDP |
| 5 | 461 | 0.63 | 0.77 | 45 | SO4, NDP |
Interfaces
8 interfaces between chains.
- P–R · 1909 Ų buried · 38 hydrogen bonds · protein-protein
- O–Q · 1859 Ų buried · 41 hydrogen bonds · protein-protein
- O–R · 1339 Ų buried · 13 hydrogen bonds · protein-protein
- P–Q · 1328 Ų buried · 17 hydrogen bonds · protein-protein
- O–P · 463 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2PKQ · Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase… · the same entry in another collection · chain T against T, TM-score 1.00
- P19866 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase a… · a predicted model of the same protein · chain S against A, TM-score 1.00
- P12860 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase B… · a predicted model of the same protein · chain Q against A, TM-score 0.98
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 P12860
- Every structure of UniProt P19866
- Elsewhere: RCSB PDB 2PKQ · PDBe 2PKQ · UniProt P12860 · UniProt P19866
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