MolNFT v1 · #143009 · protein + DNA
Structure of streptomyces venezuelae bldc-whii opt complex
6AMK · Putative DNA-binding protein: “Structure of streptomyces venezuelae bldc-whii opt complex”. X-ray diffraction, 4 pockets (best druggability 0.48). MolNFT v1 #143009 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AMK
- Type
- protein + DNA
- Length
- 147 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative DNA-binding protein; DNA (5'- D(*TP*TP*CP*AP*AP*TP*TP*CP*GP*GP*GP*TP*AP*AP*TP*TP*…
- UniProt
- A0A0M7QSG5
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative DNA-binding protein | protein | 52 | 50% helix, 17% strand | A0A0M7QSG5 |
| B | Putative DNA-binding protein | protein | 51 | 43% helix, 18% strand | A0A0M7QSG5 |
| R | DNA (5'- D(*TP*TP*CP*AP*AP*TP*TP*CP*GP*GP*GP*TP*AP*AP*TP*TP*CP*GP*GP*GP*CP*A)- 3') | dna | 22 | — | — |
| Z | DNA (5'- D(*AP*AP*TP*GP*TP*CP*CP*GP*AP*AP*TP*TP*AP*CP*CP*CP*GP*AP*AP*TP*TP*G)- 3') | dna | 22 | — | — |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.48 | 0.78 | 16 | empty |
| 2 | 153 | 0.47 | 0.77 | 18 | empty |
| 3 | 71 | 0.35 | 0.78 | 14 | empty |
| 4 | 55 | 0.32 | 0.76 | 13 | empty |
Interfaces
6 interfaces between chains.
- R–Z · 919 Ų buried · 97 hydrogen bonds · nucleic-nucleic
- A–Z · 466 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–Z · 431 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–R · 366 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 363 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 6AMK · Structure of Streptomyces venezuelae BldC-whiI opt complex · 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 A0A0M7QSG5
- Elsewhere: RCSB PDB 6AMK · PDBe 6AMK · UniProt A0A0M7QSG5
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