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
- 6GHR
- Type
- protein
- Length
- 1,446 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
- 8 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 342 | 32% helix, 27% strand | Q8DIW5 |
| C, D, A | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 338 | 32% helix, 27% strand | Q8DIW5 |
| E | CP12 polypeptide | protein | 21 | 38% helix, 0% strand | Q8DHX3 |
| F | CP12 polypeptide | protein | 69 | 71% helix, 0% strand | Q8DHX3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains B, F, C, D, A, E
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.84 | 0.85 | 111 | NAD, SO4 |
| 2 | 1025 | 0.83 | 0.84 | 110 | NAD |
| 3 | 232 | 0.83 | 0.95 | 40 | empty |
| 4 | 122 | 0.77 | 0.96 | 33 | empty |
| 5 | 421 | 0.59 | 0.75 | 38 | empty |
Interfaces
10 interfaces between chains.
- B–A · 2096 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2088 Ų buried · 30 hydrogen bonds · protein-protein
- D–A · 1287 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1280 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 794 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6GHR · 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 6GHR · PDBe 6GHR · UniProt Q8DIW5 · UniProt Q8DHX3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.