MolNFT v1 · #146807 · protein + DNA

Bacteriophage N4 RNA polymerase II and DNA complex

6DT7 · RNAP1: “Bacteriophage N4 RNA polymerase II and DNA complex”. X-ray diffraction, 6 pockets (best druggability 0.73). MolNFT v1 #146807 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DT7
Type: protein + DNA
Length: 678 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNAP1; RNAP2; DNA (5'-D(P*CP*CP*AP*CP*CP*TP*GP*CP*A)-3')
UniProt: Q8LTE4, Q8LTE3
Pockets: 6 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNAP1	protein	265	46% helix, 10% strand	Q8LTE4
B	RNAP2	protein	404	56% helix, 11% strand	Q8LTE3
C	DNA (5'-D(PCPCPAPCPCPTPGPCP*A)-3')	dna	9	—	—

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	640	0.73	0.80	56	empty
2	390	0.64	0.79	48	empty
3	93	0.45	0.80	13	empty
4	117	0.42	0.76	16	empty
5	132	0.41	0.75	17	empty

Interfaces

3 interfaces between chains.

A–B · 2846 Å² buried · 41 hydrogen bonds · protein-protein
A–C · 811 Å² buried · 8 hydrogen bonds · protein-nucleic
B–C · 305 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

6DT7 · Bacteriophage N4 RNA polymerase II and DNA 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 Q8LTE4
Every structure of UniProt Q8LTE3
Elsewhere: RCSB PDB 6DT7 · PDBe 6DT7 · UniProt Q8LTE4 · UniProt Q8LTE3

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