MolNFT v1 · #104066 · protein
The crystal structure of adenylate kinase from francisella tularensis subsp. tularensis schu S4
4PZL: “The crystal structure of adenylate kinase from francisella tularensis subsp. tularensis schu S4”. X-ray diffraction, 1 ligand (CA), 13 pockets (best druggability 0.85). MolNFT v1 #104066 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4PZL
- Type
- protein
- Length
- 892 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- Q5NFR4
- Ligands
- CA
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase (EC 2.7.4.3) | protein | 227 | 47% helix, 19% strand | Q5NFR4 |
| B | Adenylate kinase (EC 2.7.4.3) | protein | 228 | 45% helix, 19% strand | Q5NFR4 |
| C | Adenylate kinase (EC 2.7.4.3) | protein | 219 | 47% helix, 17% strand | Q5NFR4 |
| D | Adenylate kinase (EC 2.7.4.3) | protein | 218 | 47% helix, 18% strand | Q5NFR4 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
- FMT · Formic acid · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.85 | 0.86 | 131 | FMT, CA |
| 2 | 108 | 0.58 | 0.85 | 24 | GOL |
| 3 | 432 | 0.58 | 0.74 | 63 | empty |
| 4 | 253 | 0.57 | 0.78 | 27 | empty |
| 5 | 124 | 0.55 | 0.83 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1452 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1102 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 596 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 583 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 344 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4PZL · The crystal structure of adenylate kinase from Francisella tularensis subsp. tularensis… · the same entry in another collection · chain D against D, TM-score 1.00
- Q5NFR4 · AlphaFold monomer V2.0 prediction for adenylate kinase (Q5NFR4) · a predicted model of the same protein · chain C against A, TM-score 0.72
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 Q5NFR4
- Elsewhere: RCSB PDB 4PZL · PDBe 4PZL · UniProt Q5NFR4
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