Research workbench
Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from neisseria gonorrhoeae bound to NAD
Analyse Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VMT
- Type
- protein
- Length
- 2,616 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- B4RPP8
- Ligands
- NAD, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 333 | 31% helix, 28% strand | B4RPP8 |
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 334 | 29% helix, 28% strand | B4RPP8 |
| C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 325 | 28% helix, 28% strand | B4RPP8 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 334 | 29% helix, 28% strand | B4RPP8 |
| E | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 293 | 27% helix, 24% strand | B4RPP8 |
| G | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 332 | 27% helix, 29% strand | B4RPP8 |
| H | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 332 | 29% helix, 29% strand | B4RPP8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, C, B, D, E, G, F, H
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.83 | 0.84 | 105 | empty |
| 2 | 1040 | 0.83 | 0.84 | 105 | empty |
| 3 | 629 | 0.73 | 0.80 | 78 | NAD |
| 4 | 501 | 0.72 | 0.82 | 56 | NAD |
| 5 | 605 | 0.72 | 0.80 | 64 | NAD |
Interfaces
14 interfaces between chains.
- A–B · 2036 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 2031 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2019 Ų buried · 46 hydrogen bonds · protein-protein
- G–H · 1895 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 1377 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5VMT · Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria… · the same entry in another collection · chain G against G, 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 B4RPP8
- Elsewhere: RCSB PDB 5VMT · PDBe 5VMT · UniProt B4RPP8
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