Research workbench
Mtrr bound to the mtrcde operator from neisseria gonorrhoeae
Analyse Mtrr bound to the mtrcde operator from neisseria gonorrhoeae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JU3
- Type
- protein + DNA
- Length
- 447 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional regulator mtrr; DNA (5'…
- UniProt
- P39897
- Ligands
- CA
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulator mtrr | protein | 202 | 77% helix, 1% strand | P39897 |
| B | Hth-type transcriptional regulator mtrr | protein | 203 | 76% helix, 1% strand | P39897 |
| C | DNA (5'- D(*TP*AP*TP*CP*CP*GP*TP*GP*CP*AP*AP*TP*CP*GP*TP*GP*TP*AP*TP*GP*T)- 3') | dna | 21 | — | — |
| D | DNA (5'- D(*AP*CP*AP*TP*AP*CP*AP*CP*GP*AP*TP*TP*GP*CP*AP*CP*GP*GP*AP*TP*A)- 3') | dna | 21 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.66 | 0.76 | 49 | empty |
| 2 | 137 | 0.54 | 0.82 | 31 | empty |
| 3 | 104 | 0.42 | 0.78 | 19 | empty |
| 4 | 74 | 0.39 | 0.78 | 19 | empty |
| 5 | 66 | 0.31 | 0.74 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1779 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 936 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- A–C · 374 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–D · 337 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–C · 280 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 7JU3 · MtrR bound to the mtrCDE operator from Neisseria gonorrhoeae · the same entry in another collection · chain A against A, TM-score 1.00
- P39897 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator mtrr (P39897) · a predicted model of the same protein · chain B against A, TM-score 0.88
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 P39897
- Elsewhere: RCSB PDB 7JU3 · PDBe 7JU3 · UniProt P39897
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