Research workbench
Crystal structure of the binary complex, obtained by soaking, of photosyntetic A4 glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with CP12-2, both from arabidopsis thaliana.
Analyse Crystal structure of the binary complex, obtained by soaking, of photosyntetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RVD
- Type
- protein
- Length
- 3,485 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic; Photosyntetic…
- EC
- 1.2.1.13
- UniProt
- P25856, Q9LZP9
- Ligands
- NAD, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, Q | Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic (EC 1.2.1.13) | protein | 336 | 32% helix, 26% strand | P25856 |
| E | Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic (EC 1.2.1.13) | protein | 336 | 26% helix, 23% strand | P25856 |
| G, O | Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic (EC 1.2.1.13) | protein | 337 | 29% helix, 25% strand | P25856 |
| H | Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic (EC 1.2.1.13) | protein | 335 | 27% helix, 23% strand | P25856 |
| I, M | Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (A4 isoform) | protein | 22 | 36% helix, 0% strand | Q9LZP9 |
| J, K | Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (A4 isoform) | protein | 21 | 38% helix, 0% strand | Q9LZP9 |
| L | Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (A4 isoform) | protein | 19 | 32% helix, 0% strand | Q9LZP9 |
| N | Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (A4 isoform) | protein | 19 | 26% helix, 0% strand | Q9LZP9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 10 copies · chains A, D, I, B, J, C, E, H, N, F, G, M, K, O, L, Q
- SO4 · Sulfate ion · ion · 28 copies · chains A, B, C, E, D, F, G, H, O, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.84 | 0.85 | 139 | NAD, SO4 |
| 2 | 1030 | 0.83 | 0.84 | 109 | NAD, SO4 |
| 3 | 1125 | 0.82 | 0.83 | 105 | NAD, SO4 |
| 4 | 1198 | 0.81 | 0.83 | 119 | NAD, SO4 |
| 5 | 768 | 0.81 | 0.85 | 92 | empty |
Interfaces
28 interfaces between chains.
- O–Q · 1958 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1954 Ų buried · 31 hydrogen bonds · protein-protein
- F–H · 1941 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1921 Ų buried · 34 hydrogen bonds · protein-protein
- E–G · 1874 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3RVD · Crystal structure of the binary complex, obtained by soaking, of photosyntetic a4… · the same entry in another collection · chain K against K, 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 P25856
- Every structure of UniProt Q9LZP9
- Elsewhere: RCSB PDB 3RVD · PDBe 3RVD · UniProt P25856 · UniProt Q9LZP9
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