Research workbench
Crystal structure of L-allo-threonine aldolase (TM1744) from thermotoga maritima at 2.25 a resolution
Analyse Crystal structure of L-allo-threonine aldolase (TM1744) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FM1
- Type
- protein
- Length
- 1,374 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-allo-threonine aldolase
- Ligands
- CA, NA, CL
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | L-allo-threonine aldolase | protein | 343 | 47% helix, 18% strand | — |
| D | L-allo-threonine aldolase | protein | 345 | 46% helix, 17% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains D
- CL · Chloride ion · ion · 10 copies · chains A, C, D, B
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.75 | 0.97 | 24 | empty |
| 2 | 547 | 0.70 | 0.79 | 60 | CL |
| 3 | 487 | 0.68 | 0.79 | 57 | CL |
| 4 | 494 | 0.66 | 0.78 | 53 | empty |
| 5 | 509 | 0.66 | 0.77 | 54 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1932 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1926 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1006 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 981 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 807 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 2FM1 · Crystal structure of L-ALLO-threonine aldolase (tm1744) from Thermotoga maritima at 2.25… · 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
- Elsewhere: RCSB PDB 2FM1 · PDBe 2FM1
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