MolNFT v1 · #35373 · protein
Crystal structure of T.TH.HB8 argininosuccinate lyase complexed with L-arginine
2E9F: “Crystal structure of T.TH.HB8 argininosuccinate lyase complexed with L-arginine”. X-ray diffraction, 1 ligand (ARG), 16 pockets (best druggability 0.78). MolNFT v1 #35373 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2E9F
- Type
- protein
- Length
- 1,796 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argininosuccinate lyase
- EC
- 4.3.2.1
- UniProt
- Q5SLL0
- Ligands
- ARG
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argininosuccinate lyase (EC 4.3.2.1) | protein | 449 | 67% helix, 6% strand | Q5SLL0 |
| B | Argininosuccinate lyase (EC 4.3.2.1) | protein | 450 | 68% helix, 5% strand | Q5SLL0 |
| C | Argininosuccinate lyase (EC 4.3.2.1) | protein | 448 | 67% helix, 5% strand | Q5SLL0 |
| D | Argininosuccinate lyase (EC 4.3.2.1) | protein | 449 | 66% helix, 5% strand | Q5SLL0 |
Ligands and binding sites
- ARG · Arginine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.78 | 0.82 | 51 | ARG |
| 2 | 857 | 0.77 | 0.80 | 79 | ARG |
| 3 | 804 | 0.76 | 0.81 | 70 | ARG |
| 4 | 726 | 0.76 | 0.81 | 56 | ARG |
| 5 | 400 | 0.70 | 0.82 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4228 Ų buried · 68 hydrogen bonds · protein-protein
- C–D · 4154 Ų buried · 76 hydrogen bonds · protein-protein
- A–C · 1790 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1723 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1705 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2E9F · Crystal Structure of T.th.HB8 Argininosuccinate lyase complexed with L-Arginine · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SLL0 · AlphaFold monomer V2.0 prediction for argininosuccinate lyase (Q5SLL0) · a predicted model of the same protein · chain C 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 Q5SLL0
- Elsewhere: RCSB PDB 2E9F · PDBe 2E9F · UniProt Q5SLL0
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