MolNFT v1 · #150027 · protein
Cyanobacterial GAPDH with full-length CP12
6GHL · CP12 polypeptide: “Cyanobacterial GAPDH with full-length CP12”. X-ray diffraction, 1 ligand (NAD), 6 pockets (best druggability 0.85). MolNFT v1 #150027 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GHL
- Type
- protein
- Length
- 1,442 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CP12 polypeptide; Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- Q8DHX3, Q8DIW5
- Ligands
- NAD
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | CP12 polypeptide | protein | 68 | 68% helix, 0% strand | Q8DHX3 |
| E | CP12 polypeptide | protein | 21 | 38% helix, 0% strand | Q8DHX3 |
| A, B, C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 338 | 31% helix, 27% strand | Q8DIW5 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 339 | 30% helix, 28% strand | Q8DIW5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains E, A, D, F, B, C
- MLI · Malonate ion · additive · 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 | 373 | 0.85 | 0.94 | 59 | empty |
| 2 | 1057 | 0.84 | 0.85 | 114 | NAD, MLI |
| 3 | 1145 | 0.82 | 0.84 | 119 | NAD |
| 4 | 367 | 0.57 | 0.75 | 36 | empty |
| 5 | 342 | 0.55 | 0.75 | 33 | empty |
Interfaces
10 interfaces between chains.
- B–D · 2128 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2099 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1322 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1310 Ų buried · 19 hydrogen bonds · protein-protein
- F–B · 809 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6GHL · cyanobacterial GAPDH with full-length CP12 · the same entry in another collection · chain F against F, 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
- Elsewhere: RCSB PDB 6GHL · PDBe 6GHL · UniProt Q8DHX3 · UniProt Q8DIW5
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