MolNFT v2 · #153332 · protein
GAPDH of Streptococcus agalactiae
6IEP · Glyceraldehyde-3-phosphate dehydrogenase: “GAPDH of Streptococcus agalactiae”. X-ray diffraction at 2.6, 11 pockets (best druggability 0.83). MolNFT v2 #153332 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IEP
- Type
- protein
- Length
- 1,335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Streptococcus agalactiae NEM316
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- Q8E3E8
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.6 · 3 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 333 | 28% helix, 29% strand | Q8E3E8 |
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 332 | 28% helix, 28% strand | Q8E3E8 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 337 | 28% helix, 28% strand | Q8E3E8 |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.83 | 0.84 | 102 | empty |
| 2 | 893 | 0.74 | 0.78 | 110 | empty |
| 3 | 901 | 0.74 | 0.78 | 107 | empty |
| 4 | 114 | 0.43 | 0.77 | 25 | empty |
| 5 | 108 | 0.42 | 0.77 | 21 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2023 Ų buried · 52 hydrogen bonds · protein-protein
- A–D · 2006 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 1358 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1337 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 588 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6IEP · GAPDH of streptococcus agalactiae · 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 Q8E3E8
- Elsewhere: RCSB PDB 6IEP · PDBe 6IEP · UniProt Q8E3E8
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