Research workbench
Dgpb-dgpc complex apo 2.5 ångström
Analyse Dgpb-dgpc complex apo 2.5 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EXZ
- Type
- protein
- Length
- 1,850 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AP_ENDONUC_2 domain-containing protein; Dgpb
- UniProt
- A0A3Q9WXL1, A0A3Q9WUX0
- Ligands
- MN, SO4
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | AP_ENDONUC_2 domain-containing protein | protein | 324 | 52% helix, 14% strand | A0A3Q9WXL1 |
| B, H | Dgpb | protein | 139 | 7% helix, 52% strand | A0A3Q9WUX0 |
| C, E | AP_ENDONUC_2 domain-containing protein | protein | 323 | 52% helix, 15% strand | A0A3Q9WXL1 |
| D | Dgpb | protein | 138 | 9% helix, 52% strand | A0A3Q9WUX0 |
| F | Dgpb | protein | 140 | 9% helix, 51% strand | A0A3Q9WUX0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, E, G
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, E, D, G, F, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains B, D, F, H
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.77 | 0.82 | 53 | GOL |
| 2 | 802 | 0.77 | 0.81 | 64 | GOL, SO4 |
| 3 | 712 | 0.76 | 0.81 | 72 | GOL, SO4 |
| 4 | 672 | 0.75 | 0.81 | 59 | GOL |
| 5 | 616 | 0.73 | 0.80 | 73 | SO4 |
Interfaces
18 interfaces between chains.
- A–B · 1220 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1217 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1174 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1168 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 704 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7EXZ · DgpB-DgpC complex apo 2.5 angstrom · 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 A0A3Q9WXL1
- Every structure of UniProt A0A3Q9WUX0
- Elsewhere: RCSB PDB 7EXZ · PDBe 7EXZ · UniProt A0A3Q9WXL1 · UniProt A0A3Q9WUX0
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