Research workbench
Complex of O-acety-L-homoserine aminocarboxypropyltransferase (mety) from thermotoga maritima and a key reaction intermediate
Analyse Complex of O-acety-L-homoserine aminocarboxypropyltransferase (mety) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KB1
- Type
- protein
- Length
- 1,712 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-acetyl-L-homoserine sulfhydrylase
- EC
- 2.5.1.-
- UniProt
- Q9WZY4
- Ligands
- WBJ, PLP, NA, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | O-acetyl-L-homoserine sulfhydrylase (EC 2.5.1.-) | protein | 428 | 41% helix, 15% strand | Q9WZY4 |
Ligands and binding sites
- WBJ · (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid · ligand · 3 copies · chains A, B, C, D
- PLP · Pyridoxal-5'-phosphate · ligand · chains C, D
- NA · Sodium ion · metal · chains A
- MG · Magnesium ion · metal · chains D
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.78 | 0.98 | 32 | WBJ |
| 2 | 113 | 0.78 | 0.97 | 32 | WBJ |
| 3 | 103 | 0.78 | 0.98 | 31 | WBJ |
| 4 | 102 | 0.76 | 0.97 | 31 | PLP |
| 5 | 429 | 0.66 | 0.78 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3272 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3238 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 1581 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1556 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 782 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7KB1 · Complex of O-acety-L-homoserine aminocarboxypropyltransferase (MetY) from Thermotoga… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WZY4 · AlphaFold monomer V2.0 prediction for O-acetyl-L-homoserine sulfhydrylase (Q9WZY4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9WZY4
- Elsewhere: RCSB PDB 7KB1 · PDBe 7KB1 · UniProt Q9WZY4
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