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
- 6GG7
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- 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
- Pockets
- 1 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 338 | 31% helix, 28% strand | Q8DIW5 |
| C, D | CP12 polypeptide | protein | 22 | 36% helix, 0% strand | Q8DHX3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.87 | 0.89 | 129 | NAD |
Interfaces
6 interfaces between chains.
- B–A · 1287 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 845 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 821 Ų buried · 23 hydrogen bonds · protein-protein
- C–A · 274 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 269 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6GG7 · cyanobacterial GAPDH with full-length CP12 · the same entry in another collection · chain B against B, 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 6GG7 · PDBe 6GG7 · UniProt Q8DIW5 · UniProt Q8DHX3
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