MolNFT v1 · #50271 · protein

X-ray crystal structure of acrb in complex with a novel transmembrane helix.

2RDD · Acriflavine resistance protein B: “X-ray crystal structure of acrb in complex with a novel transmembrane helix.”. X-ray diffraction, 1 ligand (AIC), 20 pockets (best druggability 0.77). MolNFT v1 #50271 on GenesisL1: 3D structure…

PDB: 2RDD
Type: protein
Length: 1,055 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acriflavine resistance protein B; UPF0092 membrane protein yajc
UniProt: P31224, P0ADZ7
Ligands: AIC
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acriflavine resistance protein B	protein	1018	50% helix, 14% strand	P31224
B	UPF0092 membrane protein yajc	protein	37	81% helix, 0% strand	P0ADZ7

Ligands and binding sites

AIC · (2S,5R,6R)-6-{[(2R)-2-amino-2-phenylethanoyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid · ligand · 2 copies · chains 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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	642	0.77	0.83	83	empty
2	151	0.73	0.91	27	empty
3	659	0.73	0.79	71	empty
4	255	0.68	0.84	46	empty
5	78	0.61	0.89	17	empty

Interfaces

1 interface between chains.

A–B · 838 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2RDD · X-ray crystal structure of AcrB in complex with a novel transmembrane helix. · the same entry in another collection · chain A against A, TM-score 1.00
P31224 · AlphaFold monomer V2.0 prediction for multidrug efflux pump subunit acrb (P31224) · a predicted model of the same protein · chain A against A, TM-score 0.95
P0ADZ7 · AlphaFold monomer V2.0 prediction for sec translocon accessory complex subunit yajc… · a predicted model of the same protein · chain B against A, TM-score 0.69

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 P31224
Every structure of UniProt P0ADZ7
Elsewhere: RCSB PDB 2RDD · PDBe 2RDD · UniProt P31224 · UniProt P0ADZ7

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