Research workbench
Crystal structure of engineered bradyrhizobium japonicum GLYCINE:[CARRIER protein] ligase complexed with carrier protein from agrobacterium tumefaciens and ATP
Analyse Crystal structure of engineered bradyrhizobium japonicum GLYCINE:[CARRIER… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H2Y
- Type
- protein
- Length
- 731 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
- EC
- 6.2.1.-
- UniProt
- Q89VT8, Q7CWR3, A9CHM9
- Ligands
- ATP, PNS, ZN, MG
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amino acid--[acyl-carrier-protein] ligase 1 (EC 6.2.1.-) | protein | 295 | 41% helix, 26% strand | Q89VT8, Q7CWR3 |
| B | Amino acid--[acyl-carrier-protein] ligase 1 (EC 6.2.1.-) | protein | 296 | 39% helix, 26% strand | Q89VT8, Q7CWR3 |
| C | Aminoacyl carrier protein | protein | 77 | 61% helix, 0% strand | A9CHM9 |
| D | Aminoacyl carrier protein | protein | 63 | 54% helix, 0% strand | A9CHM9 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- PNS · 4'-phosphopantetheine · ligand · 2 copies · chains B, C, A, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.81 | 0.86 | 68 | ATP, MG, PNS |
| 2 | 794 | 0.80 | 0.83 | 82 | ATP, PNS |
| 3 | 714 | 0.76 | 0.81 | 47 | empty |
| 4 | 86 | 0.46 | 0.81 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2492 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 540 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 498 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (phosphopantetheinylation).
Compared structures
- 4H2Y · Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase… · the same entry in another collection · chain A against A, 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
- Q7CWR3 · AlphaFold monomer V2.0 prediction for amino acid--[acyl-carrier- protein] ligase (Q7CWR3) · a predicted model of the same protein · chain B against A, TM-score 0.97
- A9CHM9 · AlphaFold monomer V2.0 prediction for aminoacyl carrier protein (A9CHM9) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 Q7CWR3
- Every structure of UniProt A9CHM9
- Elsewhere: RCSB PDB 4H2Y · PDBe 4H2Y · UniProt Q89VT8 · UniProt Q7CWR3 · UniProt A9CHM9
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