Structure of PDB 2hdq Chain B

Receptor sequence

>2hdqB (length=358) Species: 83333 (Escherichia coli K-12)

APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQP
VTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNG
ITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANS
SIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPAEEKNYAWGY
REGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQ
LAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSDNKIALAARPVKAITP
PTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVDAA
WQILNALQ

3D structure

• PDB: 2hdq Deconstructing fragment-based inhibitor discovery
• Chain: B
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): S64 K67 Y112 A114 V121 Y150 G156 E272 K315 A318
• Catalytic site (residue number reindexed from 1): S61 K64 Y109 A111 V118 Y147 G153 E269 K312 A315
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

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	C21	B	P240 Q256 A307 R309 P330	P237 Q253 A304 R306 P327	MOAD: Ki=40mM BindingDB: Ki=40000000nM
BS02	C21	B	P140 W142 A143	P137 W139 A140	MOAD: Ki=40mM BindingDB: Ki=40000000nM
BS03	C21	B	V211 Y221 T319	V208 Y218 T316	MOAD: Ki=40mM BindingDB: Ki=40000000nM
BS04	C21	B	G206 K342	G203 K339	MOAD: Ki=40mM BindingDB: Ki=40000000nM
BS05	C21	B	P38 A231 R232 Q235	P35 A228 R229 Q232	MOAD: Ki=40mM BindingDB: Ki=40000000nM

Gene Ontology

Molecular Function

• GO:0008800 beta-lactamase activity
• GO:0016787 hydrolase activity

Biological Process

• GO:0017001 antibiotic catabolic process
• GO:0046677 response to antibiotic

Cellular Component

• GO:0030288 outer membrane-bounded periplasmic space
• GO:0042597 periplasmic space

External links

• PDB: RCSB:2hdq, PDBe:2hdq, PDBj:2hdq
• PDBsum: 2hdq
• PubMed: 17072304
• UniProt: P00811|AMPC_ECOLI Beta-lactamase (Gene Name=ampC)