MolNFT v1 · #139103 · protein

RNA polymerase II from komagataella pastoris (type-1 crystal)

5X4Z · DNA-directed RNA polymerase subunit: “RNA polymerase II from komagataella pastoris (type-1 crystal)”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.89). MolNFT v1 #139103 on GenesisL1: 3D structure, binding sites…

PDB: 5X4Z
Type: protein
Length: 7,637 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit beta; RNA…
EC: 2.7.7.6
UniProt: C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, C4QWA8
Ligands: ZN
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 16 distinct chains · 30% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit (EC 2.7.7.6)	protein	1384	38% helix, 14% strand	C4R4Y0
B	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1070	27% helix, 20% strand	C4QZQ7
C, O	RNA polymerase II third largest subunit B44, part of central core	protein	265	23% helix, 17% strand	C4R7L2
D	RNA polymerase II subunit B32	protein	159	43% helix, 7% strand	C4R2U9
E, Q	RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III	protein	214	32% helix, 19% strand	C4R3P8
F, R	RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III	protein	84	31% helix, 14% strand	C4R1V1
G, S	RNA polymerase II subunit	protein	171	9% helix, 44% strand	C4R9A1
H	RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III	protein	130	2% helix, 42% strand	C4R273
I, U	DNA-directed RNA polymerase subunit	protein	113	4% helix, 23% strand	F2QPE6
J, V	RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III	protein	62	44% helix, 0% strand	C4R009
K, W	RNA polymerase II subunit B12.5	protein	114	32% helix, 24% strand	C4R3Z5
L, X	RNA polymerase subunit, found in RNA polymerase complexes I, II, and III	protein	46	0% helix, 9% strand	C4QWA8
M	DNA-directed RNA polymerase subunit (EC 2.7.7.6)	protein	1387	38% helix, 14% strand	C4R4Y0
N	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1074	27% helix, 20% strand	C4QZQ7
P	RNA polymerase II subunit B32	protein	164	44% helix, 7% strand	C4R2U9
T	RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III	protein	131	2% helix, 42% strand	C4R273

Ligands and binding sites

ZN · Zinc ion · metal · 16 copies · chains A, B, D, C, I, J, L, M, N, O, U, V, X

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	1025	0.89	0.90	131	empty
2	942	0.88	0.90	127	empty
3	632	0.83	0.88	81	empty
4	878	0.82	0.84	97	empty
5	1019	0.82	0.83	133	empty

Interfaces

58 interfaces between chains.

M–N · 9124 Å² buried · 110 hydrogen bonds · protein-protein
A–B · 9036 Å² buried · 108 hydrogen bonds · protein-protein
A–E · 2108 Å² buried · 22 hydrogen bonds · protein-protein
M–Q · 2103 Å² buried · 22 hydrogen bonds · protein-protein
P–S · 1947 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5X4Z · RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) · 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 C4R4Y0
Every structure of UniProt C4QZQ7
Every structure of UniProt C4R7L2
Every structure of UniProt C4R2U9
Every structure of UniProt C4R3P8
Every structure of UniProt C4R1V1
Every structure of UniProt C4R9A1
Every structure of UniProt C4R273
Every structure of UniProt F2QPE6
Every structure of UniProt C4R009
Every structure of UniProt C4R3Z5
Every structure of UniProt C4QWA8
Elsewhere: RCSB PDB 5X4Z · PDBe 5X4Z · UniProt C4R4Y0 · UniProt C4QZQ7 · UniProt C4R7L2 · UniProt C4R2U9 · UniProt C4R3P8 · UniProt C4R1V1 · UniProt C4R9A1 · UniProt C4R273 · UniProt F2QPE6 · UniProt C4R009 · UniProt C4R3Z5 · UniProt C4QWA8

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