MolNFT v1 · #158548 · protein
Type I L-asparaginase from escherichia COLI in complex with citrate at pH 4
6NXD · L-asparaginase 1: “Type I L-asparaginase from escherichia COLI in complex with citrate at pH 4”. X-ray diffraction, 2 ligands (ASN, CL), 20 pockets (best druggability 0.83). MolNFT v1 #158548 on GenesisL1: 3D structure, binding…
- PDB
- 6NXD
- Type
- protein
- Length
- 1,265 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase 1
- EC
- 3.5.1.1
- UniProt
- P0A962
- Ligands
- ASN, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase 1 (EC 3.5.1.1) | protein | 305 | 30% helix, 24% strand | P0A962 |
| B | L-asparaginase 1 (EC 3.5.1.1) | protein | 325 | 32% helix, 23% strand | P0A962 |
| C | L-asparaginase 1 (EC 3.5.1.1) | protein | 311 | 32% helix, 24% strand | P0A962 |
| D | L-asparaginase 1 (EC 3.5.1.1) | protein | 324 | 32% helix, 23% strand | P0A962 |
Ligands and binding sites
- ASN · Asparagine · ligand · 4 copies · chains A, C, B, D
- CL · Chloride ion · ion · 10 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, C, B, D
- CIT · Citric acid · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.83 | 0.97 | 50 | ASN, EDO |
| 2 | 214 | 0.83 | 0.97 | 43 | ASN, EDO |
| 3 | 222 | 0.78 | 0.92 | 38 | empty |
| 4 | 255 | 0.74 | 0.88 | 36 | empty |
| 5 | 908 | 0.74 | 0.78 | 93 | CL |
Interfaces
6 interfaces between chains.
- A–C · 1787 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1750 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1190 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1075 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 234 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 6NXD · Type I L-asparaginase from escherichia COLI in complex with citrate at pH 4 · the same entry in another collection · chain D against D, TM-score 1.00
- P0A962 · AlphaFold monomer V2.0 prediction for L-asparaginase 1 (P0A962) · 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 P0A962
- Elsewhere: RCSB PDB 6NXD · PDBe 6NXD · UniProt P0A962
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