Research workbench
Crystal structure of glutamine-dependent NAD+ synthetase from M. tuberculosis bound to AMP/PPI, NAD+, and glutamate
Analyse Crystal structure of glutamine-dependent NAD+ synthetase from M. tuberculosis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SYT
- Type
- protein
- Length
- 2,620 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine-dependent NAD(+) synthetase
- EC
- 6.3.5.1
- UniProt
- P0A5L6
- Ligands
- GLU, NAD, AMP, POP
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 660 | 43% helix, 18% strand | P0A5L6 |
| C | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 651 | 44% helix, 18% strand | P0A5L6 |
| D | Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 649 | 44% helix, 18% strand | P0A5L6 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, D, C
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.81 | 0.84 | 68 | GLU |
| 2 | 875 | 0.81 | 0.83 | 68 | GLU |
| 3 | 122 | 0.81 | 0.99 | 41 | empty |
| 4 | 133 | 0.80 | 0.97 | 42 | empty |
| 5 | 881 | 0.73 | 0.77 | 91 | NAD, AMP, POP |
Interfaces
5 interfaces between chains.
- B–D · 3955 Ų buried · 73 hydrogen bonds · protein-protein
- A–D · 1913 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1901 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1550 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1536 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3SYT · Crystal structure of glutamine-dependent NAD+ synthetase from M. tuberculosis bound to… · the same entry in another collection · chain C against C, 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 P0A5L6
- Elsewhere: RCSB PDB 3SYT · PDBe 3SYT · UniProt P0A5L6
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