Research workbench
Crystal structure of a bacterial dehydrogenase at 2.19 ångströms resolution
Analyse Crystal structure of a bacterial dehydrogenase at 2.19 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LD5
- Type
- protein
- Length
- 1,363 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- F1T6A5
- Ligands
- NAD
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 341 | 28% helix, 28% strand | F1T6A5 |
| B, D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 340 | 28% helix, 29% strand | F1T6A5 |
| C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 342 | 28% helix, 28% strand | F1T6A5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 12 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1176 | 0.80 | 0.81 | 123 | NAD, GOL |
| 2 | 1069 | 0.80 | 0.81 | 102 | GOL |
| 3 | 1198 | 0.80 | 0.81 | 126 | NAD |
| 4 | 110 | 0.41 | 0.76 | 16 | GOL |
| 5 | 97 | 0.40 | 0.77 | 18 | GOL |
Interfaces
6 interfaces between chains.
- A–C · 1920 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1895 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1396 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1393 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 604 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5LD5 · Crystal structure of a bacterial dehydrogenase at 2.19 Angstroms resolution · 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 F1T6A5
- Elsewhere: RCSB PDB 5LD5 · PDBe 5LD5 · UniProt F1T6A5
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