Research workbench
GAPDH-CP12-prk complex
Analyse GAPDH-CP12-prk complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GVE
- Type
- protein
- Length
- 4,272 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CP12 polypeptide; Glyceraldehyde-3-phosphate dehydrogenase; Phosphoribulokinase
- EC
- 1.2.1.-, 2.7.1.19
- UniProt
- Q8DHX3, Q8DIW5, Q8DHN2
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, C, H, M | CP12 polypeptide | protein | 75 | 68% helix, 0% strand | Q8DHX3 |
| D, A, E, F, I, K, N, O | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 337 | 28% helix, 28% strand | Q8DIW5 |
| J, B, G, L | Phosphoribulokinase (EC 2.7.1.19) | protein | 319 | 30% helix, 25% strand | Q8DHN2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains P, D, A, E, F, C, I, K, H, N, O, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.84 | 0.85 | 128 | NAD |
| 2 | 1082 | 0.83 | 0.84 | 138 | NAD |
| 3 | 1142 | 0.83 | 0.84 | 132 | NAD |
| 4 | 219 | 0.82 | 0.95 | 45 | empty |
| 5 | 465 | 0.81 | 0.89 | 60 | NAD |
Interfaces
34 interfaces between chains.
- A–F · 2154 Ų buried · 25 hydrogen bonds · protein-protein
- K–O · 2135 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 2118 Ų buried · 20 hydrogen bonds · protein-protein
- I–N · 2117 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1407 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6GVE · GAPDH-CP12-PRK complex · the same entry in another collection · chain P against P, 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 Q8DHX3
- Every structure of UniProt Q8DIW5
- Every structure of UniProt Q8DHN2
- Elsewhere: RCSB PDB 6GVE · PDBe 6GVE · UniProt Q8DHX3 · UniProt Q8DIW5 · UniProt Q8DHN2
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