Research workbench
Structure of GAPDH with CP12 peptide from thermosynechococcus elongatus
Analyse Structure of GAPDH with CP12 peptide from thermosynechococcus elongatus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZDF
- 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
- 1.2.1.13
- UniProt
- Q8DIW5, Q8DHX3
- Ligands
- NAD
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.13) | protein | 338 | 31% helix, 27% strand | Q8DIW5 |
| C | CP12 polypeptide | protein | 21 | 38% helix, 0% strand | Q8DHX3 |
| D | CP12 polypeptide | protein | 23 | 35% helix, 0% strand | Q8DHX3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.73 | 0.78 | 85 | NAD |
| 2 | 559 | 0.72 | 0.81 | 64 | NAD |
| 3 | 354 | 0.55 | 0.74 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–D · 830 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 819 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 514 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3ZDF · Structure of GAPDH with CP12 peptide from Thermosynechococcus elongatus · 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 3ZDF · PDBe 3ZDF · UniProt Q8DIW5 · UniProt Q8DHX3
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