Research workbench
Crystal structure of S.AUREUS glyceraldehyde-3-phosphate-dehydrogenase (gap) containing oxidized CYS151
Analyse Crystal structure of S.AUREUS glyceraldehyde-3-phosphate-dehydrogenase (gap)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T73
- Type
- protein
- Length
- 1,340 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase 1
- EC
- 1.2.1.12
- UniProt
- Q6GIL8
- Ligands
- NA
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 335 | 28% helix, 29% strand | Q6GIL8 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.73 | 0.81 | 63 | empty |
| 2 | 495 | 0.70 | 0.80 | 59 | empty |
| 3 | 549 | 0.68 | 0.78 | 68 | empty |
| 4 | 458 | 0.65 | 0.78 | 54 | empty |
| 5 | 440 | 0.65 | 0.78 | 58 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2148 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2135 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 1425 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1401 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 624 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 5T73 · Crystal structure of S.aureus glyceraldehyde-3-phosphate-dehydrogenase (Gap) containing… · the same entry in another collection · chain D against D, TM-score 1.00
- Q6GIL8 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase 1 (Q6GIL8) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q6GIL8
- Elsewhere: RCSB PDB 5T73 · PDBe 5T73 · UniProt Q6GIL8
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