Research workbench

The P-lobe of RNA polymerase II pre-initiation complex

Analyse The P-lobe of RNA polymerase II pre-initiation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FMF
Type: protein + DNA
Length: 6,715 residues
Chains: 27
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair helicase RAD25, SSL2; Transcription elongation factor S-II, DST1; DNA-directed…
EC: 3.6.4.12, 2.7.7.6
UniProt: Q00578, P07273, P04050, P08518, P16370, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P32774, P29055, P13393, P36100, P36145, P41896, Q02939, Q3E7C1, P06839
Ligands: ZN, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 27 distinct chains · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	DNA repair helicase RAD25, SSL2 (EC 3.6.4.12)	protein	473	37% helix, 19% strand	Q00578
2	Transcription elongation factor S-II, DST1	protein	174	7% helix, 6% strand	P07273
A	DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6)	protein	1422	41% helix, 17% strand	P04050
B	DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6)	protein	1156	28% helix, 26% strand	P08518
C	DNA-directed RNA polymerase II subunit RPB3	protein	266	26% helix, 29% strand	P16370
D	RNA polymerase II pre-initiation complex, RPB4	protein	178	49% helix, 7% strand	—
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1, RPB5	protein	214	41% helix, 24% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2, RPB6	protein	84	35% helix, 15% strand	P20435
G	DNA-directed RNA polymerase II subunit RPB7	protein	171	13% helix, 50% strand	P34087
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3, RPB8	protein	133	2% helix, 43% strand	P20436
I	DNA-directed RNA polymerase II subunit RPB9	protein	119	4% helix, 30% strand	P27999
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5, RPB10	protein	65	45% helix, 2% strand	P22139
K	DNA-directed RNA polymerase II subunit RPB11	protein	114	40% helix, 24% strand	P38902
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4, RPB12	protein	46	0% helix, 13% strand	P40422
M	RNA polymerase II pre-initiation complex, TOA1	protein	116	41% helix, 32% strand	—
N	Non-template strand DNA	dna	72	—	—
O	Transcription initiation factor iia subunit 2, TOA2	protein	101	40% helix, 38% strand	P32774
P	Transcription initiation factor iib, SUA7	protein	293	45% helix, 1% strand	P29055
Q	Tata-box-binding protein, tbp	protein	180	27% helix, 41% strand	P13393
R	Transcription initiation factor iie subunit alpha, TFA1	protein	118	45% helix, 21% strand	P36100
S	Transcription initiation factor iie subunit beta, TFA2	protein	121	51% helix, 12% strand	P36145
T	Template strand DNA	dna	72	—	—
U	RNA polymerase II pre-initiation complex, TFG1	protein	150	17% helix, 43% strand	—
V	Transcription initiation factor iif subunit beta, TFG2 (EC 3.6.4.12)	protein	174	29% helix, 33% strand	P41896
W	RNA polymerase II transcription factor B subunit 2, TFB2	protein	62	44% helix, 31% strand	Q02939
X	RNA polymerase II transcription factor B subunit 5, TFB5	protein	63	48% helix, 30% strand	Q3E7C1
Y	DNA repair helicase RAD3 (EC 3.6.4.12)	protein	578	54% helix, 14% strand	P06839

Ligands and binding sites

ZN · Zinc ion · metal · 9 copies · chains 2, A, B, C, I, J, L
MG · Magnesium ion · metal · 2 copies · chains 2, A

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	779	0.89	0.92	98	empty
2	1117	0.84	0.85	123	empty
3	916	0.83	0.85	72	empty
4	567	0.82	0.88	69	empty
5	636	0.81	0.86	60	empty

Interfaces

65 interfaces between chains.

A–B · 9792 Å² buried · 156 hydrogen bonds · protein-protein
N–T · 3014 Å² buried · 183 hydrogen bonds · nucleic-nucleic
M–O · 2830 Å² buried · 39 hydrogen bonds · protein-protein
2–A · 2495 Å² buried · 58 hydrogen bonds · protein-protein
D–G · 2466 Å² buried · 35 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 isopeptide, 3 disulfide (isopeptide, disulfide).

Compared structures

5FMF · the P-lobe of RNA polymerase II pre-initiation complex · the same entry in another collection · chain D against D, 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 Q00578
Every structure of UniProt P07273
Every structure of UniProt P04050
Every structure of UniProt P08518
Every structure of UniProt P16370
Every structure of UniProt P20434
Every structure of UniProt P20435
Every structure of UniProt P34087
Every structure of UniProt P20436
Every structure of UniProt P27999
Every structure of UniProt P22139
Every structure of UniProt P38902
Every structure of UniProt P40422
Every structure of UniProt P32774
Every structure of UniProt P29055
Every structure of UniProt P13393
Every structure of UniProt P36100
Every structure of UniProt P36145
Every structure of UniProt P41896
Every structure of UniProt Q02939
Every structure of UniProt Q3E7C1
Every structure of UniProt P06839
Elsewhere: RCSB PDB 5FMF · PDBe 5FMF · UniProt Q00578 · UniProt P07273 · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P32774 · UniProt P29055 · UniProt P13393 · UniProt P36100 · UniProt P36145 · UniProt P41896 · UniProt Q02939 · UniProt Q3E7C1 · UniProt P06839

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