MolNFT v1 · #163793 · protein + DNA
Crystal structure of the DNA binding domain of M. polymorpha auxin response factor 2 (MPARF2) in complex with high affinity DNA
6SDG: “Crystal structure of the DNA binding domain of M. polymorpha auxin response factor 2 (MPARF2) in complex with…”. X-ray diffraction, 12 pockets (best druggability 0.76). MolNFT v1 #163793 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6SDG
- Type
- protein + DNA
- Length
- 674 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Auxin response factor; 21-7_A; 21-7_B
- UniProt
- A0A0K2QVG1
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Auxin response factor | protein | 318 | 19% helix, 30% strand | A0A0K2QVG1 |
| B | Auxin response factor | protein | 314 | 21% helix, 29% strand | A0A0K2QVG1 |
| C | 21-7_A | dna | 21 | — | — |
| D | 21-7_B | dna | 21 | — | — |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.76 | 0.80 | 59 | empty |
| 2 | 726 | 0.69 | 0.77 | 71 | empty |
| 3 | 131 | 0.66 | 0.89 | 22 | empty |
| 4 | 249 | 0.65 | 0.82 | 32 | empty |
| 5 | 72 | 0.57 | 0.89 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1364 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 967 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- B–C · 540 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 532 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–D · 451 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 6SDG · Crystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2… · 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 A0A0K2QVG1
- Elsewhere: RCSB PDB 6SDG · PDBe 6SDG · UniProt A0A0K2QVG1
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