Research workbench
Crystal structure of the putative pyrophosphatase ypjd from bacillus subtilis. northeast structural genomics consortium target SR428.
Analyse Crystal structure of the putative pyrophosphatase ypjd from bacillus subtilis.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GTA
- Type
- protein
- Length
- 377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein ypjd
- UniProt
- P42979
- Ligands
- NA
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein ypjd | protein | 98 | 64% helix, 1% strand | P42979 |
| B | Hypothetical protein ypjd | protein | 96 | 70% helix, 1% strand | P42979 |
| C | Hypothetical protein ypjd | protein | 86 | 77% helix, 1% strand | P42979 |
| D | Hypothetical protein ypjd | protein | 97 | 73% helix, 1% strand | P42979 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.47 | 0.77 | 14 | empty |
| 2 | 141 | 0.46 | 0.76 | 20 | empty |
| 3 | 78 | 0.43 | 0.79 | 13 | empty |
| 4 | 71 | 0.39 | 0.79 | 18 | empty |
| 5 | 67 | 0.36 | 0.78 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2430 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 2249 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 753 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 573 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 208 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 2GTA · Crystal Structure of the putative pyrophosphatase YPJD from Bacillus subtilis. Northeast… · the same entry in another collection · chain D against D, TM-score 1.00
- P42979 · AlphaFold monomer V2.0 prediction for uncharacterized protein ypjd (P42979) · a predicted model of the same protein · chain C 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 P42979
- Elsewhere: RCSB PDB 2GTA · PDBe 2GTA · UniProt P42979
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