Research workbench
Crystal structure of bradyrhizobium japonicum GLYCINE:[CARRIER protein] ligase complexed with glycylated carrier protein
Analyse Crystal structure of bradyrhizobium japonicum GLYCINE:[CARRIER protein] ligase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H2V
- Type
- protein
- Length
- 692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amino acid--[acyl-carrier-protein] ligase 1; Aminoacyl carrier protein 1
- EC
- 6.2.1.-
- UniProt
- Q89VT8, Q89VT6
- Ligands
- AMP, H2V, PNS, ZN, SO4, PO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amino acid--[acyl-carrier-protein] ligase 1 (EC 6.2.1.-) | protein | 295 | 40% helix, 27% strand | Q89VT8 |
| B | Amino acid--[acyl-carrier-protein] ligase 1 (EC 6.2.1.-) | protein | 297 | 39% helix, 27% strand | Q89VT8 |
| C | Aminoacyl carrier protein 1 | protein | 26 | 31% helix, 0% strand | Q89VT6 |
| D | Aminoacyl carrier protein 1 | protein | 74 | 54% helix, 3% strand | Q89VT6 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- H2V · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] aminoethanethioate · ligand · chains A, C
- PNS · 4'-phosphopantetheine · ligand · chains B, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B
- PO4 · Phosphate ion · ion · chains B
- ACT · Acetate ion · additive · 3 copies · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.80 | 0.85 | 62 | AMP, PO4, PNS |
| 2 | 609 | 0.79 | 0.85 | 59 | AMP, H2V |
| 3 | 724 | 0.78 | 0.82 | 47 | empty |
| 4 | 51 | 0.29 | 0.75 | 16 | empty |
| 5 | 53 | 0.28 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2484 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 620 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 537 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 covalent (phosphopantetheinylation, covalent ligand).
Compared structures
- 4H2V · Crystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed… · the same entry in another collection · chain D against D, TM-score 1.00
- Q89VT8 · AlphaFold monomer V2.0 prediction for amino acid--[acyl-carrier- protein] ligase 1… · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q89VT6 · AlphaFold monomer V2.0 prediction for aminoacyl carrier protein 1 (Q89VT6) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q89VT8
- Every structure of UniProt Q89VT6
- Elsewhere: RCSB PDB 4H2V · PDBe 4H2V · UniProt Q89VT8 · UniProt Q89VT6
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