MolNFT v1 · #38306 · protein
Crystal structure of the putative pyrophosphatase ypjd from bacillus subtilis. northeast structural genomics consortium target SR428.
2GTA · Hypothetical protein ypjd: “Crystal structure of the putative pyrophosphatase ypjd from bacillus subtilis. northeast structural genomics…”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.47). MolNFT v1 #38306 on…
- 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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