Research workbench
Cyanobacterial GAPDH with full-length CP12
Analyse Cyanobacterial GAPDH with full-length CP12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GFO
- Type
- protein
- Length
- 1,495 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase; CP12 polypeptide
- EC
- 1.2.1.-
- UniProt
- Q8DIW5, Q8DHX3
- Ligands
- NAD, SO4
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 338 | 31% helix, 26% strand | Q8DIW5 |
| E | CP12 polypeptide | protein | 75 | 71% helix, 0% strand | Q8DHX3 |
| F | CP12 polypeptide | protein | 68 | 66% helix, 0% strand | Q8DHX3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, E, B, C, F
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.85 | 0.94 | 55 | empty |
| 2 | 1058 | 0.83 | 0.84 | 112 | NAD, SO4 |
| 3 | 1066 | 0.83 | 0.84 | 121 | NAD |
| 4 | 441 | 0.60 | 0.75 | 54 | empty |
| 5 | 388 | 0.58 | 0.76 | 37 | empty |
Interfaces
10 interfaces between chains.
- A–C · 2127 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 2106 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1303 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1297 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 822 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6GFO · cyanobacterial GAPDH with full-length CP12 · 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 Q8DIW5
- Every structure of UniProt Q8DHX3
- Elsewhere: RCSB PDB 6GFO · PDBe 6GFO · UniProt Q8DIW5 · UniProt Q8DHX3
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