Structure of PDB 5bot Chain A

Receptor sequence
>5botA (length=166) Species: 9606 (Homo sapiens) [Search protein sequence]
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGFMLPD
DDVQGIQSLYGPGDED
3D structure
PDB5bot Fragment-based discovery of indole inhibitors of matrix metalloproteinase-13.
ChainA
Resolution1.85 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) H222 E223 H226 H232
Catalytic site (residue number reindexed from 1) H119 E120 H123 H129
Enzyme Commision number 3.4.24.-
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 4UM A H222 A238 L239 F241 P242 T245 T247 H119 A135 L136 F138 P139 T142 T144 MOAD: ic50=39uM
PDBbind-CN: -logKd/Ki=4.41,IC50=39uM
BindingDB: IC50=39000nM
BS02 ZN A H222 H226 H232 H119 H123 H129
BS03 ZN A H172 D174 H187 H200 H69 D71 H84 H97
BS04 CA A D128 D203 E205 D25 D100 E102
BS05 CA A D179 G180 S182 L184 D202 E205 D76 G77 S79 L81 D99 E102
BS06 CA A D162 N194 G196 D198 D59 N91 G93 D95
Gene Ontology
Molecular Function
GO:0004222 metalloendopeptidase activity
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0031012 extracellular matrix

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5bot, PDBe:5bot, PDBj:5bot
PDBsum5bot
PubMed22017539
UniProtP45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)

[Back to BioLiP]