MolNFT v1 · #67518 · protein

Crystal structure of the NUSB101-S10(DELTA loop) complex

3IMQ · N utilization substance protein B: “Crystal structure of the NUSB101-S10(DELTA loop) complex”. X-ray diffraction, 1 ligand (K), 5 pockets (best druggability 0.70). MolNFT v1 #67518 on GenesisL1: 3D structure, binding sites and…

PDB: 3IMQ
Type: protein
Length: 672 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N utilization substance protein B; 30S ribosomal protein S10
UniProt: P0A780, P0A7R5
Ligands: K
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 58% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	N utilization substance protein B	protein	137	74% helix, 0% strand	P0A780
J, K, L	30S ribosomal protein S10	protein	87	33% helix, 36% strand	P0A7R5

Ligands and binding sites

K · Potassium ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	828	0.70	0.76	68	empty
2	65	0.61	0.91	19	empty
3	77	0.50	0.84	21	empty
4	113	0.40	0.75	18	empty
5	77	0.35	0.76	18	empty

Interfaces

6 interfaces between chains.

C–L · 905 Å² buried · 12 hydrogen bonds · protein-protein
A–J · 886 Å² buried · 11 hydrogen bonds · protein-protein
B–K · 858 Å² buried · 14 hydrogen bonds · protein-protein
J–L · 852 Å² buried · 15 hydrogen bonds · protein-protein
J–B · 445 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3IMQ · Crystal structure of the NusB101-S10(delta loop) complex · the same entry in another collection · chain B against B, TM-score 1.00
P0A780 · AlphaFold monomer V2.0 prediction for transcription antitermination protein nusb (P0A780) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P0A780
Every structure of UniProt P0A7R5
Elsewhere: RCSB PDB 3IMQ · PDBe 3IMQ · UniProt P0A780 · UniProt P0A7R5

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