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Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph methylacidiphilum fumariolicum solv
Analyse Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T3T
- Type
- protein
- Length
- 1,200 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- I0JZ23
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 300 | 52% helix, 14% strand | I0JZ23 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.78 | 0.83 | 90 | SO4 |
| 2 | 435 | 0.73 | 0.83 | 63 | SO4 |
| 3 | 266 | 0.61 | 0.80 | 44 | empty |
| 4 | 206 | 0.60 | 0.81 | 32 | SO4 |
| 5 | 170 | 0.60 | 0.83 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1514 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1455 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1143 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 1073 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6T3T · Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic… · the same entry in another collection · chain B against B, 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 I0JZ23
- Elsewhere: RCSB PDB 6T3T · PDBe 6T3T · UniProt I0JZ23
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