Research workbench
Crystal structure of mutant R43D/C273S of L-asparaginase I from yersinia pestis
Analyse Crystal structure of mutant R43D/C273S of L-asparaginase I from yersinia pestis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R69
- Type
- protein
- Length
- 1,242 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase I
- EC
- 3.5.1.1
- UniProt
- A0A3N4B0Q2
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase I (EC 3.5.1.1) | protein | 319 | 34% helix, 21% strand | A0A3N4B0Q2 |
| B | L-asparaginase I (EC 3.5.1.1) | protein | 312 | 34% helix, 20% strand | A0A3N4B0Q2 |
| C | L-asparaginase I (EC 3.5.1.1) | protein | 308 | 34% helix, 20% strand | A0A3N4B0Q2 |
| D | L-asparaginase I (EC 3.5.1.1) | protein | 303 | 34% helix, 21% strand | A0A3N4B0Q2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.82 | 0.95 | 49 | EDO |
| 2 | 207 | 0.82 | 0.96 | 37 | EDO |
| 3 | 523 | 0.73 | 0.82 | 49 | empty |
| 4 | 620 | 0.73 | 0.80 | 53 | empty |
| 5 | 209 | 0.49 | 0.75 | 33 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2050 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2022 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 614 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7R69 · Crystal structure of mutant R43D/C273S of L-Asparaginase I from Yersinia pestis · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A3N4B0Q2
- Elsewhere: RCSB PDB 7R69 · PDBe 7R69 · UniProt A0A3N4B0Q2
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