MolNFT v1 · #61531 · protein
Crystal structure of trka glyceraldehyde-3-phosphate dehydrogenase from brucella melitensis
3DOC · Glyceraldehyde 3-phosphate dehydrogenase: “Crystal structure of trka glyceraldehyde-3-phosphate dehydrogenase from brucella melitensis”. X-ray diffraction, 1 ligand (NAD), 4 pockets (best druggability 0.81). MolNFT v1 #61531 on…
- PDB
- 3DOC
- Type
- protein
- Length
- 1,339 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde 3-phosphate dehydrogenase
- Ligands
- NAD
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glyceraldehyde 3-phosphate dehydrogenase | protein | 335 | 28% helix, 27% strand | — |
| D | Glyceraldehyde 3-phosphate dehydrogenase | protein | 334 | 31% helix, 26% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.81 | 0.84 | 88 | empty |
| 2 | 1065 | 0.78 | 0.80 | 127 | NAD |
| 3 | 520 | 0.69 | 0.79 | 53 | NAD |
| 4 | 394 | 0.66 | 0.79 | 47 | NAD |
Interfaces
6 interfaces between chains.
- A–C · 1912 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1909 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1378 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1355 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 608 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3DOC · Crystal Structure of TrkA glyceraldehyde-3-phosphate dehydrogenase from Brucella… · 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
- Elsewhere: RCSB PDB 3DOC · PDBe 3DOC
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