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Cyrstal structure of threonine-sensitive aspartokinase from methanococcus jannaschii with mgamp-pnp and L-aspartate
Analyse Cyrstal structure of threonine-sensitive aspartokinase from methanococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C1M
- Type
- protein
- Length
- 1,864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable aspartokinase
- EC
- 2.7.2.4
- UniProt
- Q57991
- Ligands
- ASP, ANP, MG
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable aspartokinase (EC 2.7.2.4) | protein | 465 | 44% helix, 23% strand | Q57991 |
| C | Probable aspartokinase (EC 2.7.2.4) | protein | 468 | 43% helix, 23% strand | Q57991 |
| D | Probable aspartokinase (EC 2.7.2.4) | protein | 466 | 44% helix, 22% strand | Q57991 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 4 copies · chains A, B, C, D
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 6 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.78 | 0.80 | 93 | MG, ASP, ANP |
| 2 | 951 | 0.78 | 0.80 | 92 | MG, ASP, ANP |
| 3 | 1095 | 0.77 | 0.80 | 98 | MG, ASP, ANP |
| 4 | 1159 | 0.76 | 0.78 | 95 | MG, ASP, ANP |
| 5 | 88 | 0.43 | 0.79 | 13 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2970 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 2946 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 565 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 536 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3C1M · Cyrstal Structure of threonine-sensitive aspartokinase from Methanococcus jannaschii with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q57991 · AlphaFold monomer V2.0 prediction for probable aspartokinase (Q57991) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q57991
- Elsewhere: RCSB PDB 3C1M · PDBe 3C1M · UniProt Q57991
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