MolNFT v1 · #99319 · protein

Nucleotide-induced asymmetry within ATPase activator ring drives S54- rnap interaction and ATP hydrolysis

4LZZ · Transcriptional regulator (ntrc family): “Nucleotide-induced asymmetry within ATPase activator ring drives S54- rnap interaction and ATP hydrolysis”. X-ray diffraction, 3 ligands (08T, ADP, MG), 20 pockets (best druggability 0.84).…

PDB: 4LZZ
Type: protein
Length: 5,941 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulator (ntrc family)
UniProt: O67198
Ligands: 08T, ADP, MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, G, H, J, K, M, N, O, P, Q, R, S, T, U, V	Transcriptional regulator (ntrc family)	protein	247	45% helix, 15% strand	O67198
E	Transcriptional regulator (ntrc family)	protein	258	43% helix, 16% strand	O67198
I	Transcriptional regulator (ntrc family)	protein	248	45% helix, 15% strand	O67198
L, X	Transcriptional regulator (ntrc family)	protein	246	45% helix, 15% strand	O67198
W	Transcriptional regulator (ntrc family)	protein	250	44% helix, 15% strand	O67198

Ligands and binding sites

08T · [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium · ligand · 22 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains F, L
MG · Magnesium ion · metal · 23 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, N, O, P, Q, R, S, T, U, V, W, 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	976	0.84	0.85	128	08T, MG
2	805	0.82	0.84	102	ADP
3	860	0.82	0.84	69	08T, MG
4	96	0.78	0.98	21	empty
5	89	0.78	0.99	20	empty

Interfaces

28 interfaces between chains.

D–E · 1751 Å² buried · 17 hydrogen bonds · protein-protein
V–W · 1736 Å² buried · 20 hydrogen bonds · protein-protein
J–K · 1736 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1716 Å² buried · 28 hydrogen bonds · protein-protein
E–F · 1714 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4LZZ · Nucleotide-induced asymmetry within atpase activator ring drives s54-RNAP interaction and… · 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 O67198
Elsewhere: RCSB PDB 4LZZ · PDBe 4LZZ · UniProt O67198

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