Research workbench
Determinants of enzyme thermostability observed in the molecular structure of thermus aquaticus D-glyceraldehyde- 3-phosphate dehydrogenase at 2.5 ångströms resolution
Analyse Determinants of enzyme thermostability observed in the molecular structure of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CER
- Type
- protein
- Length
- 2,648 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holo-D-glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- P00361
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P, Q, R, A, B, C, D | Holo-D-glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 331 | 30% helix, 27% strand | P00361 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains O, R, P, Q, A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.86 | 0.92 | 57 | empty |
| 2 | 607 | 0.84 | 0.89 | 65 | empty |
| 3 | 554 | 0.70 | 0.79 | 59 | NAD |
| 4 | 511 | 0.69 | 0.79 | 58 | NAD |
| 5 | 543 | 0.69 | 0.79 | 58 | NAD |
Interfaces
15 interfaces between chains.
- A–B · 2124 Ų buried · 31 hydrogen bonds · protein-protein
- O–P · 2118 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2084 Ų buried · 27 hydrogen bonds · protein-protein
- Q–R · 2078 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1437 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1CER · Determinants of enzyme thermostability observed in the molecular structure of thermus… · the same entry in another collection · chain C against C, TM-score 1.00
- P00361 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P00361) · a predicted model of the same protein · chain O 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 P00361
- Elsewhere: RCSB PDB 1CER · PDBe 1CER · UniProt P00361
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