Research workbench
Dgpb-dgpc complex apo
Analyse Dgpb-dgpc complex apo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BVR
- Type
- protein
- Length
- 1,848 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
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | AP_ENDONUC_2 domain-containing protein | protein | 323 | 52% helix, 14% strand | A0A3Q9WXL1 |
| B, H | Dgpb | protein | 139 | 7% helix, 52% strand | A0A3Q9WUX0 |
| D | Dgpb | protein | 138 | 9% helix, 52% strand | A0A3Q9WUX0 |
| F | Dgpb | protein | 140 | 7% helix, 50% strand | A0A3Q9WUX0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, E, G
- 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
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 | 708 | 0.77 | 0.82 | 71 | GOL |
| 2 | 914 | 0.77 | 0.80 | 76 | empty |
| 3 | 818 | 0.77 | 0.80 | 69 | GOL |
| 4 | 700 | 0.77 | 0.82 | 60 | GOL |
| 5 | 701 | 0.74 | 0.80 | 57 | GOL |
Interfaces
18 interfaces between chains.
- A–B · 1220 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1219 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1198 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1174 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 712 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7BVR · DgpB-DgpC complex apo · 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 7BVR · PDBe 7BVR · UniProt A0A3Q9WXL1 · UniProt A0A3Q9WUX0
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