Research workbench
Crystal structure of argininosuccinate synthase from legionella pneumophila philadelphia 1 in complex with anppnp and a substrate analogue arginine
Analyse Crystal structure of argininosuccinate synthase from legionella pneumophila… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K5Z
- Type
- protein
- Length
- 1,558 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argininosuccinate synthase
- EC
- 6.3.4.5
- UniProt
- Q5ZY78
- Ligands
- ANP, ARG, MG
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argininosuccinate synthase (EC 6.3.4.5) | protein | 390 | 43% helix, 20% strand | Q5ZY78 |
| B, C | Argininosuccinate synthase (EC 6.3.4.5) | protein | 390 | 43% helix, 20% strand | Q5ZY78 |
| D | Argininosuccinate synthase (EC 6.3.4.5) | protein | 388 | 44% helix, 20% strand | Q5ZY78 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- ARG · Arginine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.86 | 0.90 | 75 | EDO |
| 2 | 634 | 0.86 | 0.90 | 70 | EDO |
| 3 | 490 | 0.82 | 0.88 | 63 | empty |
| 4 | 456 | 0.81 | 0.88 | 58 | empty |
| 5 | 629 | 0.74 | 0.81 | 54 | ANP, ARG, MG |
Interfaces
6 interfaces between chains.
- A–B · 3752 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 3711 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 1054 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1026 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 890 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7K5Z · Crystal Structure of Argininosuccinate synthase from Legionella pneumophila Philadelphia… · the same entry in another collection · chain C against C, TM-score 1.00
- Q5ZY78 · AlphaFold monomer V2.0 prediction for argininosuccinate synthase (Q5ZY78) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q5ZY78
- Elsewhere: RCSB PDB 7K5Z · PDBe 7K5Z · UniProt Q5ZY78
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