MolNFT v1 · #54051 · protein
Nucleotide-bound structures of bacillus subtilis glycinamide ribonucleotide synthetase
2XD4 · Phosphoribosylamine--glycine ligase: “Nucleotide-bound structures of bacillus subtilis glycinamide ribonucleotide synthetase”. X-ray diffraction, 2 ligands (ADP, MG), 2 pockets (best druggability 0.74). MolNFT v1 #54051 on…
- PDB
- 2XD4
- Type
- protein
- Length
- 421 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylamine--glycine ligase
- EC
- 6.3.4.13
- UniProt
- P12039
- Ligands
- ADP, MG
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylamine--glycine ligase (EC 6.3.4.13) | protein | 421 | 32% helix, 29% strand | P12039 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.74 | 0.78 | 89 | MG, ADP |
| 2 | 103 | 0.34 | 0.73 | 18 | empty |
Compared structures
- 2XD4 · Nucleotide-bound Structures of Bacillus subtilis Glycinamide Ribonucleotide Synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- P12039 · AlphaFold monomer V2.0 prediction for phosphoribosylamine--glycine ligase (P12039) · 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 P12039
- Elsewhere: RCSB PDB 2XD4 · PDBe 2XD4 · UniProt P12039
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