Research workbench
Crystal structure of engineered bradyrhizobium japonicum GLYCINE:[CARRIER protein] ligase complexed with carrier protein from agrobacterium tumefaciens and an analogue of glycyl adenylate
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
- 4H2X
- Type
- protein
- Length
- 743 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
- G5A, PNS, ZN, CL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 44% 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 | 40% helix, 27% strand | Q89VT8, Q7CWR3 |
| B | Amino acid--[acyl-carrier-protein] ligase 1 (EC 6.2.1.-) | protein | 296 | 40% helix, 25% strand | Q89VT8, Q7CWR3 |
| C | Aminoacyl carrier protein | protein | 77 | 61% helix, 0% strand | A9CHM9 |
| D | Aminoacyl carrier protein | protein | 75 | 53% helix, 0% strand | A9CHM9 |
Ligands and binding sites
- G5A · 5'-O-(glycylsulfamoyl)adenosine · ligand · 2 copies · chains A, B
- PNS · 4'-phosphopantetheine · ligand · 2 copies · chains B, C, A, D
- ZN · Zinc ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.82 | 0.85 | 83 | G5A, CL, PNS |
| 2 | 696 | 0.81 | 0.85 | 75 | G5A, CL, PNS |
| 3 | 648 | 0.77 | 0.83 | 45 | empty |
| 4 | 66 | 0.48 | 0.84 | 19 | empty |
| 5 | 90 | 0.47 | 0.81 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2524 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 630 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 618 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 modified (phosphopantetheinylation, oxidation).
Compared structures
- 4H2X · Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase… · the same entry in another collection · chain C against C, 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 0.97
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 4H2X · PDBe 4H2X · UniProt Q89VT8 · UniProt Q7CWR3 · UniProt A9CHM9
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