MolNFT v1 · #176577 · protein
Cryo-EM structure of dgpb-C at 2.85 ångström resolution
7DRD · AP_ENDONUC_2 domain-containing protein: “Cryo-EM structure of dgpb-C at 2.85 ångström resolution”. Electron microscopy, 17 pockets (best druggability 0.82). MolNFT v1 #176577 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7DRD
- Type
- protein
- Length
- 1,604 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AP_ENDONUC_2 domain-containing protein; Dgpb
- UniProt
- A0A3Q9WXL1, A0A3Q9WUX0
- Pockets
- 17 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AP_ENDONUC_2 domain-containing protein | protein | 261 | 47% helix, 18% strand | A0A3Q9WXL1 |
| B, D, F, H | Dgpb | protein | 137 | 7% helix, 51% strand | A0A3Q9WUX0 |
| C, E | AP_ENDONUC_2 domain-containing protein | protein | 264 | 47% helix, 19% strand | A0A3Q9WXL1 |
| G | AP_ENDONUC_2 domain-containing protein | protein | 267 | 47% helix, 19% strand | A0A3Q9WXL1 |
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.82 | 0.83 | 102 | empty |
| 2 | 532 | 0.78 | 0.84 | 60 | empty |
| 3 | 579 | 0.74 | 0.81 | 73 | empty |
| 4 | 554 | 0.73 | 0.81 | 74 | empty |
| 5 | 388 | 0.73 | 0.84 | 53 | empty |
Interfaces
18 interfaces between chains.
- G–H · 1149 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1142 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1140 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1128 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 686 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7DRD · Cryo-EM structure of DgpB-C at 2.85 angstrom resolution · 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 7DRD · PDBe 7DRD · UniProt A0A3Q9WXL1 · UniProt A0A3Q9WUX0
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