MolNFT v1 · #140455 · protein + DNA
X-ray structure of ets domain of ERGP55 in complex with E74DNA
5YBD · Transcriptional regulator erg: “X-ray structure of ets domain of ERGP55 in complex with E74DNA”. X-ray diffraction, 2 pockets (best druggability 0.69). MolNFT v1 #140455 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YBD
- Type
- protein + DNA
- Length
- 228 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator erg; DNA (5'-D(P*AP*CP*CP*GP*GP*AP*AP*GP*T)-3'); DNA…
- UniProt
- P11308
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator erg | protein | 96 | 54% helix, 13% strand | P11308 |
| B, Y | DNA (5'-D(P*AP*CP*CP*GP*GP*AP*AP*GP*T)-3') | dna | 9 | — | — |
| C, Z | DNA (5'-D(P*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3') | dna | 10 | — | — |
| X | Transcriptional regulator erg | protein | 94 | 50% helix, 13% strand | P11308 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.69 | 0.85 | 26 | empty |
| 2 | 126 | 0.42 | 0.76 | 16 | empty |
Interfaces
13 interfaces between chains.
- X–Z · 535 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 506 Ų buried · 13 hydrogen bonds · protein-nucleic
- X–Y · 448 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 430 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 424 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Compared structures
- 5YBD · X-ray structure of ETS domain of Ergp55 in complex with E74DNA · the same entry in another collection · chain Z against Z, TM-score 1.00
- P11308 · AlphaFold monomer V2.0 prediction for transcriptional regulator erg (P11308) · a predicted model of the same protein · chain X against A, TM-score 0.92
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 P11308
- Elsewhere: RCSB PDB 5YBD · PDBe 5YBD · UniProt P11308
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