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Structure of an enterococcus faecalis hd-domain protein complexed with dgtp and datp
Analyse Structure of an enterococcus faecalis hd-domain protein complexed with dgtp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IRH
- Type
- protein
- Length
- 1,783 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hd domain protein
- UniProt
- Q836G9
- Ligands
- DGT, DTP, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hd domain protein | protein | 450 | 55% helix, 12% strand | Q836G9 |
| B | Hd domain protein | protein | 445 | 56% helix, 11% strand | Q836G9 |
| C | Hd domain protein | protein | 454 | 55% helix, 12% strand | Q836G9 |
| D | Hd domain protein | protein | 434 | 59% helix, 12% strand | Q836G9 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains B, D
- CA · Calcium 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
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 | 317 | 0.85 | 0.96 | 40 | empty |
| 2 | 270 | 0.84 | 0.95 | 34 | empty |
| 3 | 531 | 0.77 | 0.84 | 44 | empty |
| 4 | 547 | 0.76 | 0.83 | 57 | empty |
| 5 | 905 | 0.75 | 0.78 | 71 | DGT |
Interfaces
6 interfaces between chains.
- A–B · 1920 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1881 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1092 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1016 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 848 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3IRH · Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dATP · 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 Q836G9
- Elsewhere: RCSB PDB 3IRH · PDBe 3IRH · UniProt Q836G9
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