Research workbench

Transcription termination intermediate complex 5

Analyse Transcription termination intermediate complex 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z9T
Type: protein + DNA + RNA
Length: 6,397 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription termination factor rho; Transcription TERMINATION/ANTITERMINATION protein…
EC: 3.6.4.-, 2.7.7.6
UniProt: A0A0A0GPI6, C3SSN7, P0A7Z4, P0A800, P0A8V4, C3SIA2
Ligands: ADP, BEF, DT, DA, MG, ZN
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 10 distinct chains · 33% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
f, a, b, c, d, e	Transcription termination factor rho (EC 3.6.4.-)	protein	417	39% helix, 21% strand	A0A0A0GPI6
A	Transcription TERMINATION/ANTITERMINATION protein nusa	protein	495	34% helix, 13% strand	C3SSN7
U	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	235	20% helix, 33% strand	P0A7Z4
V	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	321	28% helix, 21% strand	P0A7Z4
W	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	79	65% helix, 0% strand	P0A800
X	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	30% helix, 20% strand	P0A8V4
Y	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1343	34% helix, 13% strand	C3SIA2
L	Template strand	dna	33	—	—
K	Non template strand	dna	21	—	—
R	Rut RNA	rna	28	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains f, a, b, c, d, e
BEF · Beryllium trifluoride ion · ligand · 5 copies · chains f, a, b, c, d, e
DT · Thymidine-5'-monophosphate · ligand · 2 copies · chains Y, a, L
DA · 2'-deoxyadenosine-5'-monophosphate · ligand · chains Y
MG · Magnesium ion · metal · 6 copies · chains a, b, c, d, e, Y
ZN · Zinc ion · metal · 2 copies · chains Y

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	989	0.85	0.86	100	empty
2	870	0.82	0.84	73	empty
3	1037	0.82	0.83	85	empty
4	1020	0.81	0.82	90	empty
5	473	0.79	0.87	61	empty

Interfaces

39 interfaces between chains.

X–Y · 8164 Å² buried · 95 hydrogen bonds · protein-protein
U–V · 2522 Å² buried · 22 hydrogen bonds · protein-protein
U–X · 1990 Å² buried · 28 hydrogen bonds · protein-protein
a–b · 1681 Å² buried · 21 hydrogen bonds · protein-protein
f–a · 1668 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent (covalent ligand).

Compared structures

P0A8V4 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V4) · a predicted model of the same protein · chain X against A, TM-score 0.96
P0A800 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P0A800) · a predicted model of the same protein · chain W against A, TM-score 0.91
P0A7Z4 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P0A7Z4) · a predicted model of the same protein · chain U against A, TM-score 0.85

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 A0A0A0GPI6
Every structure of UniProt C3SSN7
Every structure of UniProt P0A7Z4
Every structure of UniProt P0A800
Every structure of UniProt P0A8V4
Every structure of UniProt C3SIA2
Elsewhere: RCSB PDB 6Z9T · PDBe 6Z9T · UniProt A0A0A0GPI6 · UniProt C3SSN7 · UniProt P0A7Z4 · UniProt P0A800 · UniProt P0A8V4 · UniProt C3SIA2

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