MolNFT v1 · #101180 · protein

RNA polymerase interacting protein ykzg from geobacillus stearothermophilus

4NJC · Geobacillus stearothermophilus ykzg: “RNA polymerase interacting protein ykzg from geobacillus stearothermophilus”. X-ray diffraction, 4 pockets (best druggability 0.78). MolNFT v1 #101180 on GenesisL1: 3D structure, binding sites…

PDB: 4NJC
Type: protein
Length: 408 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Geobacillus stearothermophilus ykzg
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 7 distinct chains · 16% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Geobacillus stearothermophilus ykzg	protein	60	13% helix, 48% strand	—
B, D	Geobacillus stearothermophilus ykzg	protein	51	16% helix, 57% strand	—
C	Geobacillus stearothermophilus ykzg	protein	48	17% helix, 52% strand	—
E	Geobacillus stearothermophilus ykzg	protein	51	16% helix, 53% strand	—
F	Geobacillus stearothermophilus ykzg	protein	49	16% helix, 51% strand	—
G	Geobacillus stearothermophilus ykzg	protein	47	17% helix, 51% strand	—
H	Geobacillus stearothermophilus ykzg	protein	51	16% helix, 53% strand	—

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	978	0.78	0.80	82	empty
2	138	0.53	0.81	19	empty
3	199	0.52	0.78	22	empty
4	171	0.51	0.78	21	empty

Interfaces

12 interfaces between chains.

B–F · 785 Å² buried · 15 hydrogen bonds · protein-protein
C–E · 762 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 687 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 673 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 394 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

4NJC · RNA Polymerase interacting protein YkzG from Geobacillus stearothermophilus · 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
Elsewhere: RCSB PDB 4NJC · PDBe 4NJC

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