Research workbench
Crystal structure of a two-domain ider-DNA complex crystal form II
Analyse Crystal structure of a two-domain ider-DNA complex crystal form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IT0
- Type
- protein + DNA
- Length
- 630 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MBTA/MBTB operator strand 1; MBTA/MBTB operator strand 2; Iron-dependent repressor ider
- UniProt
- P0A672
- Ligands
- NI
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | MBTA/MBTB operator strand 1 | dna | 33 | — | — |
| F | MBTA/MBTB operator strand 2 | dna | 33 | — | — |
| A, B | Iron-dependent repressor ider | protein | 145 | 58% helix, 6% strand | P0A672 |
| C, D | Iron-dependent repressor ider | protein | 137 | 63% helix, 6% strand | P0A672 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 12 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.72 | 0.76 | 73 | empty |
| 2 | 242 | 0.45 | 0.73 | 21 | empty |
| 3 | 225 | 0.44 | 0.72 | 22 | empty |
| 4 | 101 | 0.39 | 0.76 | 18 | empty |
| 5 | 94 | 0.36 | 0.75 | 16 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1478 Ų buried · 138 hydrogen bonds · nucleic-nucleic
- A–B · 859 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 835 Ų buried · 16 hydrogen bonds · protein-protein
- E–B · 485 Ų buried · 12 hydrogen bonds · protein-nucleic
- F–A · 421 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 2IT0 · Crystal structure of a two-domain IdeR-DNA complex crystal form II · the same entry in another collection · chain E against E, 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 P0A672
- Elsewhere: RCSB PDB 2IT0 · PDBe 2IT0 · UniProt P0A672
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.