Research workbench
Crystal structure of (A+CTE)4 chimeric form of photosyntetic glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP
Analyse Crystal structure of (A+CTE)4 chimeric form of photosyntetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PKR
- Type
- protein
- Length
- 4,041 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase aor
- EC
- 1.2.1.13
- UniProt
- P19866
- Ligands
- NDP, SO4
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, R, P, Q, A, B, C, I, M | Glyceraldehyde-3-phosphate dehydrogenase aor (EC 1.2.1.13) | protein | 337 | 30% helix, 26% strand | P19866 |
| D, H, L | Glyceraldehyde-3-phosphate dehydrogenase aor (EC 1.2.1.13) | protein | 336 | 30% helix, 26% strand | P19866 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 12 copies · chains O, R, P, Q, A, B, C, D, H, I, L, M
- SO4 · Sulfate ion · ion · 34 copies · chains O, R, P, Q, A, B, C, D, H, I, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.82 | 0.95 | 40 | empty |
| 2 | 206 | 0.81 | 0.95 | 41 | empty |
| 3 | 1048 | 0.81 | 0.82 | 114 | SO4, NDP |
| 4 | 179 | 0.80 | 0.95 | 35 | empty |
| 5 | 942 | 0.80 | 0.82 | 113 | SO4, NDP |
Interfaces
20 interfaces between chains.
- I–M · 2054 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2034 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 2030 Ų buried · 40 hydrogen bonds · protein-protein
- H–L · 2019 Ų buried · 39 hydrogen bonds · protein-protein
- O–P · 2007 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2PKR · Crystal structure of (A+CTE)4 chimeric form of photosyntetic glyceraldehyde-3-phosphate… · the same entry in another collection · chain M against M, 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 P19866
- Elsewhere: RCSB PDB 2PKR · PDBe 2PKR · UniProt P19866
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