MolNFT v1 · #104714 · protein

Crystal structure of euryarchaeal RNA polymerase from thermococcus kodakarensis

4QIW · DNA-directed RNA polymerase: “Crystal structure of euryarchaeal RNA polymerase from thermococcus kodakarensis”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.82). MolNFT v1 #104714 on GenesisL1: 3D…

PDB: 4QIW
Type: protein
Length: 6,385 residues
Chains: 22
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase; DNA-directed RNA polymerase subunit a''; DNA-directed RNA…
EC: 2.7.7.6
UniProt: Q5JE33, Q5JE32, Q5JE34, Q5JJF4, Q5JIY4, Q5JI52, Q5JE31, Q5JJD0, Q5JE88, Q5JJC9, Q5JDM8
Ligands: ZN, MG
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 12 distinct chains · 33% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase (EC 2.7.7.6)	protein	863	36% helix, 14% strand	Q5JE33
B, J	DNA-directed RNA polymerase (EC 2.7.7.6)	protein	1069	29% helix, 22% strand	Q5JE32
C, M	DNA-directed RNA polymerase subunit a'' (EC 2.7.7.6)	protein	369	39% helix, 7% strand	Q5JE34
D, O	DNA-directed RNA polymerase subunit D (EC 2.7.7.6)	protein	258	26% helix, 37% strand	Q5JJF4
E, Q	DNA-directed RNA polymerase, subunit E'	protein	181	16% helix, 48% strand	Q5JIY4
F, R	DNA-directed RNA polymerase, subunit F	protein	122	55% helix, 7% strand	Q5JI52
H, S	DNA-directed RNA polymerase subunit H (EC 2.7.7.6)	protein	76	25% helix, 30% strand	Q5JE31
K, T	DNA-directed RNA polymerase subunit K (EC 2.7.7.6)	protein	56	46% helix, 5% strand	Q5JJD0
L, U	DNA-directed RNA polymerase subunit L (EC 2.7.7.6)	protein	94	37% helix, 24% strand	Q5JE88
N, V	DNA-directed RNA polymerase subunit N (EC 2.7.7.6)	protein	63	48% helix, 0% strand	Q5JJC9
P, W	DNA-directed RNA polymerase subunit P (EC 2.7.7.6)	protein	42	0% helix, 12% strand	Q5JDM8
I	DNA-directed RNA polymerase (EC 2.7.7.6)	protein	862	35% helix, 15% strand	Q5JE33

Ligands and binding sites

ZN · Zinc ion · metal · 10 copies · chains A, B, N, P, I, J, V, W
MG · Magnesium ion · metal · 4 copies · chains A, B, I, J

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	952	0.82	0.84	107	empty
2	1048	0.81	0.82	96	empty
3	244	0.80	0.93	31	empty
4	857	0.79	0.82	86	empty
5	924	0.79	0.81	88	empty

Interfaces

54 interfaces between chains.

A–B · 7133 Å² buried · 84 hydrogen bonds · protein-protein
I–J · 7071 Å² buried · 88 hydrogen bonds · protein-protein
A–C · 4575 Å² buried · 40 hydrogen bonds · protein-protein
I–M · 4471 Å² buried · 34 hydrogen bonds · protein-protein
Q–R · 2392 Å² buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4QIW · Crystal structure of euryarchaeal RNA polymerase from Thermococcus kodakarensis · the same entry in another collection · chain P against P, 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 Q5JE33
Every structure of UniProt Q5JE32
Every structure of UniProt Q5JE34
Every structure of UniProt Q5JJF4
Every structure of UniProt Q5JIY4
Every structure of UniProt Q5JI52
Every structure of UniProt Q5JE31
Every structure of UniProt Q5JJD0
Every structure of UniProt Q5JE88
Every structure of UniProt Q5JJC9
Every structure of UniProt Q5JDM8
Elsewhere: RCSB PDB 4QIW · PDBe 4QIW · UniProt Q5JE33 · UniProt Q5JE32 · UniProt Q5JE34 · UniProt Q5JJF4 · UniProt Q5JIY4 · UniProt Q5JI52 · UniProt Q5JE31 · UniProt Q5JJD0 · UniProt Q5JE88 · UniProt Q5JJC9 · UniProt Q5JDM8

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