Research workbench
2.05 ångström resolution crystal structure of C-terminal domain (DUF2156) of putative lysylphosphatidylglycerol synthetase from agrobacterium fabrum.
Analyse 2.05 ångström resolution crystal structure of C-terminal domain (DUF2156) of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VRV
- Type
- protein
- Length
- 1,899 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein regulated by acid pH
- UniProt
- A9CHP8
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein regulated by acid pH | protein | 319 | 45% helix, 27% strand | A9CHP8 |
| B | Protein regulated by acid pH | protein | 316 | 44% helix, 27% strand | A9CHP8 |
| C | Protein regulated by acid pH | protein | 316 | 44% helix, 26% strand | A9CHP8 |
| D | Protein regulated by acid pH | protein | 315 | 43% helix, 27% strand | A9CHP8 |
| E | Protein regulated by acid pH | protein | 316 | 43% helix, 26% strand | A9CHP8 |
| F | Protein regulated by acid pH | protein | 317 | 43% helix, 27% strand | A9CHP8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.78 | 0.94 | 32 | empty |
| 2 | 663 | 0.76 | 0.82 | 86 | GOL |
| 3 | 644 | 0.76 | 0.81 | 87 | empty |
| 4 | 640 | 0.75 | 0.81 | 89 | empty |
| 5 | 550 | 0.74 | 0.82 | 73 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1490 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1458 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1426 Ų buried · 28 hydrogen bonds · protein-protein
- A–F · 384 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 182 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 5VRV · 2.05 Angstrom Resolution Crystal Structure of C-terminal Domain (DUF2156) of Putative… · the same entry in another collection · chain A against A, TM-score 1.00
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 A9CHP8
- Elsewhere: RCSB PDB 5VRV · PDBe 5VRV · UniProt A9CHP8
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