MolNFT v1 · #12695 · protein
Crystal structure of thermus thermophilus HB8 argininosuccinate synthetase in complex with inhibitors
1KOR: “Crystal structure of thermus thermophilus HB8 argininosuccinate synthetase in complex with inhibitors”. X-ray diffraction, 2 ligands (ANP, ARG), 13 pockets (best druggability 0.90). MolNFT v1 #12695 on GenesisL1: 3D structure…
- PDB
- 1KOR
- Type
- protein
- Length
- 1,538 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argininosuccinate synthetase
- EC
- 6.3.4.5
- UniProt
- P59846
- Ligands
- ANP, ARG
- Pockets
- 13 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argininosuccinate synthetase (EC 6.3.4.5) | protein | 380 | 46% helix, 21% strand | P59846 |
| B, C, D | Argininosuccinate synthetase (EC 6.3.4.5) | protein | 386 | 46% helix, 21% strand | P59846 |
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
- SIN · Succinic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.90 | 0.95 | 75 | empty |
| 2 | 1092 | 0.89 | 0.90 | 113 | empty |
| 3 | 1143 | 0.88 | 0.90 | 122 | empty |
| 4 | 641 | 0.76 | 0.82 | 54 | ANP, ARG, SIN |
| 5 | 792 | 0.76 | 0.80 | 83 | ANP, ARG, SIN |
Interfaces
6 interfaces between chains.
- C–D · 4838 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 4530 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 1273 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1249 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 911 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1KOR · Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P59846 · AlphaFold monomer V2.0 prediction for argininosuccinate synthase (P59846) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P59846
- Elsewhere: RCSB PDB 1KOR · PDBe 1KOR · UniProt P59846
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