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Hc-J4 RNA polymerase complexed with UTP

Analyse Hc-J4 RNA polymerase complexed with UTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NB6
Type: protein
Length: 1,131 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyprotein
EC: 2.7.7.48
UniProt: Q02828
Ligands: UTP, MN
Pockets: 12 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polyprotein (EC 2.7.7.48)	protein	566	46% helix, 16% strand	Q02828
B	Polyprotein (EC 2.7.7.48)	protein	565	48% helix, 15% strand	Q02828

Ligands and binding sites

UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1115	0.81	0.82	83	MN, UTP
2	1104	0.80	0.81	91	MN, UTP
3	628	0.66	0.76	67	empty
4	304	0.56	0.76	40	empty
5	132	0.49	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 427 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1NB6 · HC-J4 RNA polymerase complexed with UTP · 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 Q02828
Elsewhere: RCSB PDB 1NB6 · PDBe 1NB6 · UniProt Q02828

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