MolNFT v1 · #58369 · protein
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase complexed with CP12 in the absence of copper from synechococcus elongatus
3B1K · Glyceraldehyde 3-phosphate dehydrogenase (NADP+): “Crystal structure of glyceraldehyde-3-phosphate dehydrogenase complexed with CP12 in the absence of copper…”. X-ray diffraction, 1 ligand (NAD), 12 pockets (best druggability 0.86).…
- PDB
- 3B1K
- Type
- protein
- Length
- 1,442 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde 3-phosphate dehydrogenase (NADP+); CP12
- EC
- 1.2.1.13
- UniProt
- Q9R6W2, Q6BBK3
- Ligands
- NAD
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, H | Glyceraldehyde 3-phosphate dehydrogenase (NADP+) (EC 1.2.1.13) | protein | 338 | 23% helix, 24% strand | Q9R6W2 |
| C, I | CP12 | protein | 22 | 32% helix, 0% strand | Q6BBK3 |
| D, J | CP12 | protein | 23 | 0% helix, 0% strand | Q6BBK3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, H, J, B, D, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.86 | 0.93 | 61 | empty |
| 2 | 1070 | 0.86 | 0.87 | 140 | NAD |
| 3 | 543 | 0.80 | 0.87 | 75 | NAD |
| 4 | 522 | 0.80 | 0.86 | 70 | NAD |
| 5 | 349 | 0.57 | 0.76 | 52 | empty |
Interfaces
16 interfaces between chains.
- A–G · 1932 Ų buried · 28 hydrogen bonds · protein-protein
- B–H · 1838 Ų buried · 26 hydrogen bonds · protein-protein
- B–G · 1386 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 1345 Ų buried · 22 hydrogen bonds · protein-protein
- G–I · 851 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3B1K · Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with CP12 in the… · the same entry in another collection · chain A against A, 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 Q9R6W2
- Every structure of UniProt Q6BBK3
- Elsewhere: RCSB PDB 3B1K · PDBe 3B1K · UniProt Q9R6W2 · UniProt Q6BBK3
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