Research workbench
Antphd with 15BP di-thioate modified DNA duplex
Analyse Antphd with 15BP di-thioate modified DNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XIC
- Type
- protein + DNA
- Length
- 175 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeotic protein antennapedia; DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C2S)…
- UniProt
- P02833
- Ligands
- NI
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeotic protein antennapedia | protein | 59 | 71% helix, 0% strand | P02833 |
| B, E | DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C2S) P*AP*TP*TP*AP*GP*AP*G)-3') | dna | 15 | — | — |
| C, F | DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)- 3') | dna | 15 | — | — |
| D | Homeotic protein antennapedia | protein | 56 | 75% helix, 0% strand | P02833 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains B, D, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.60 | 0.74 | 46 | MPD |
| 2 | 99 | 0.50 | 0.82 | 14 | empty |
| 3 | 120 | 0.49 | 0.81 | 16 | empty |
| 4 | 129 | 0.43 | 0.76 | 14 | empty |
| 5 | 62 | 0.29 | 0.75 | 12 | empty |
Interfaces
7 interfaces between chains.
- A–B · 679 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 644 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- E–F · 623 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- D–E · 488 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 474 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
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 P02833
- Elsewhere: RCSB PDB 4XIC · PDBe 4XIC · UniProt P02833
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