Structure of PDB 4pfd Chain B

Receptor sequence

>4pfdB (length=410) Species: 83332 (Mycobacterium tuberculosis H37Rv)

TTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGL
GRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAAL
PFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADG
EIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVT
ASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQL
PAKLRSEPLKFKSGTYRGKVQNLTQFYHAGFLQYQFVIPTEAVDEFKKII
GVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVS
ELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFA
SDMARRLELL

3D structure

• PDB: 4pfd Crystal structure of M. tuberculosis in complex with a cBT
• Chain: B
• Resolution: 2.3 Å

Enzymatic activity

• Enzyme Commision number: 1.1.98.3: decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	FAD	B	W16 A53 G55 L56 G57 R58 S59 Y60 N63 A64 P116 G117 T118 V121 T122 G124 G125 A128 C129 I131 H132 N178 G179 I184 Y415	W10 A47 G49 L50 G51 R52 S53 Y54 N57 A58 P110 G111 T112 V115 T116 G118 G119 A122 C123 I125 H126 N172 G173 I178 Y364
BS02	2R2	B	G117 H132 K134 S228 Y314 V365 N385 C387 D389 K418	G111 H126 K128 S222 Y277 V314 N334 C336 D338 K367

Gene Ontology

Molecular Function

• GO:0003885 D-arabinono-1,4-lactone oxidase activity
• GO:0016491 oxidoreductase activity
• GO:0050660 flavin adenine dinucleotide binding
• GO:0071949 FAD binding

Biological Process

• GO:0035884 arabinan biosynthetic process
• GO:0045227 capsule polysaccharide biosynthetic process
• GO:0046677 response to antibiotic
• GO:0070592 cell wall polysaccharide biosynthetic process
• GO:0071555 cell wall organization

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0042597 periplasmic space

External links

• PDB: RCSB:4pfd, PDBe:4pfd, PDBj:4pfd
• PDBsum: 4pfd
• UniProt: P9WJF1|DPRE1_MYCTU Decaprenylphosphoryl-beta-D-ribose oxidase (Gene Name=dprE1)