Research workbench
Crystal structure of NAD kinase 1 from listeria monocytogenes in complex with a novel inhibitor
Analyse Crystal structure of NAD kinase 1 from listeria monocytogenes in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DHQ
- Type
- protein
- Length
- 1,036 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD kinase 1
- EC
- 2.7.1.23
- UniProt
- Q8Y8D7
- Ligands
- 5AK
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD kinase 1 (EC 2.7.1.23) | protein | 263 | 21% helix, 44% strand | Q8Y8D7 |
| B | NAD kinase 1 (EC 2.7.1.23) | protein | 260 | 20% helix, 38% strand | Q8Y8D7 |
| C | NAD kinase 1 (EC 2.7.1.23) | protein | 260 | 22% helix, 41% strand | Q8Y8D7 |
| D | NAD kinase 1 (EC 2.7.1.23) | protein | 253 | 20% helix, 38% strand | Q8Y8D7 |
Ligands and binding sites
- 5AK · 8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl) sulfanyl]adenosine · ligand · 4 copies · chains A, C, B, D
- CIT · Citric acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.84 | 0.85 | 95 | GOL |
| 2 | 1185 | 0.79 | 0.81 | 97 | 5AK |
| 3 | 1160 | 0.79 | 0.80 | 88 | 5AK |
| 4 | 157 | 0.66 | 0.87 | 31 | empty |
| 5 | 189 | 0.62 | 0.83 | 29 | CIT |
Interfaces
6 interfaces between chains.
- A–B · 1292 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1289 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 823 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 789 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DHQ · Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel… · the same entry in another collection · chain B against B, 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 Q8Y8D7
- Elsewhere: RCSB PDB 5DHQ · PDBe 5DHQ · UniProt Q8Y8D7
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