Research workbench
Crystal structure of triosephosphate isomerase from burkholderia thailandensis
Analyse Crystal structure of triosephosphate isomerase from burkholderia thailandensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G1K
- Type
- protein
- Length
- 986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- Q2SZN7
- Ligands
- NA
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Triosephosphate isomerase (EC 5.3.1.1) | protein | 248 | 45% helix, 16% strand | Q2SZN7 |
| D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 242 | 45% helix, 17% strand | Q2SZN7 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.74 | 0.77 | 94 | EDO |
| 2 | 54 | 0.63 | 0.94 | 22 | empty |
| 3 | 97 | 0.48 | 0.81 | 27 | empty |
| 4 | 131 | 0.47 | 0.78 | 25 | empty |
| 5 | 125 | 0.45 | 0.78 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1795 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1783 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 514 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 97 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 94 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4G1K · Crystal structure of triosephosphate isomerase from Burkholderia thailandensis · 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 Q2SZN7
- Elsewhere: RCSB PDB 4G1K · PDBe 4G1K · UniProt Q2SZN7
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