Research workbench
Crystal structure of arabidopsis thaliana transcription factor LEC2- DNA complex
Analyse Crystal structure of arabidopsis thaliana transcription factor LEC2- DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J9C
- Type
- protein + DNA
- Length
- 283 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B3 domain-containing transcription factor LEC2; DNA…
- UniProt
- Q1PFR7
- Pockets
- 4 · best druggability 0.44
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B3 domain-containing transcription factor LEC2 | protein | 111 | 13% helix, 41% strand | Q1PFR7 |
| B, E | DNA (5'-D(*GP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)- 3') | dna | 15 | — | — |
| C, F | DNA (5'-D(*CP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)- 3') | dna | 15 | — | — |
| D | B3 domain-containing transcription factor LEC2 | protein | 112 | 11% helix, 42% strand | Q1PFR7 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.44 | 0.77 | 22 | empty |
| 2 | 64 | 0.36 | 0.78 | 18 | empty |
| 3 | 93 | 0.32 | 0.73 | 15 | empty |
| 4 | 52 | 0.23 | 0.72 | 14 | empty |
Interfaces
7 interfaces between chains.
- E–F · 636 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- B–C · 594 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–C · 521 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–F · 485 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 461 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6J9C · Crystal structure of Arabidopsis thaliana transcription factor LEC2-DNA complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q1PFR7 · AlphaFold monomer V2.0 prediction for B3 domain-containing transcription factor LEC2… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q1PFR7
- Elsewhere: RCSB PDB 6J9C · PDBe 6J9C · UniProt Q1PFR7
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