MolNFT v1 · #178853 · protein + DNA
Mtrr bound to the rpoh operator from neisseria gonorrhoeae
7JNP · Hth-type transcriptional regulator mtrr: “Mtrr bound to the rpoh operator from neisseria gonorrhoeae”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.67). MolNFT v1 #178853 on GenesisL1: 3D structure, binding sites…
- PDB
- 7JNP
- Type
- protein + DNA
- Length
- 445 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
- 5 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulator mtrr | protein | 202 | 77% helix, 1% strand | P39897 |
| C | DNA (5'- D(*TP*TP*AP*CP*AP*TP*AP*CP*AP*AP*CP*CP*AP*CP*GP*TP*AP*TP*GP*TP*A)- 3') | dna | 21 | — | — |
| D | DNA (5'- D(*TP*AP*CP*AP*TP*AP*CP*GP*TP*GP*GP*TP*TP*GP*TP*AP*TP*GP*TP*AP*A)- 3') | dna | 21 | — | — |
| B | Hth-type transcriptional regulator mtrr | protein | 201 | 77% helix, 1% strand | P39897 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.67 | 0.76 | 50 | empty |
| 2 | 87 | 0.43 | 0.79 | 18 | empty |
| 3 | 83 | 0.41 | 0.78 | 18 | empty |
| 4 | 72 | 0.36 | 0.77 | 19 | empty |
| 5 | 55 | 0.29 | 0.75 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1817 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 931 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- A–D · 372 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–B · 340 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–B · 282 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 7JNP · MtrR bound to the rpoH operator from Neisseria gonorrhoeae · the same entry in another collection · chain B against B, 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 A 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 7JNP · PDBe 7JNP · UniProt P39897
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