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4R8I

High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2

Functional Information from GO Data
ChainGOidnamespacecontents
A0001525biological_processangiogenesis
A0002548biological_processmonocyte chemotaxis
A0004672molecular_functionprotein kinase activity
A0005102molecular_functionsignaling receptor binding
A0005125molecular_functioncytokine activity
A0005515molecular_functionprotein binding
A0005576cellular_componentextracellular region
A0005615cellular_componentextracellular space
A0006468biological_processprotein phosphorylation
A0006935biological_processchemotaxis
A0006954biological_processinflammatory response
A0006955biological_processimmune response
A0006959biological_processhumoral immune response
A0007010biological_processcytoskeleton organization
A0007155biological_processcell adhesion
A0007165biological_processsignal transduction
A0007166biological_processcell surface receptor signaling pathway
A0007186biological_processG protein-coupled receptor signaling pathway
A0007187biological_processG protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger
A0007259biological_processcell surface receptor signaling pathway via JAK-STAT
A0008009molecular_functionchemokine activity
A0008360biological_processregulation of cell shape
A0009617biological_processresponse to bacterium
A0009887biological_processanimal organ morphogenesis
A0019079biological_processviral genome replication
A0019221biological_processcytokine-mediated signaling pathway
A0019233biological_processsensory perception of pain
A0019725biological_processcellular homeostasis
A0030335biological_processpositive regulation of cell migration
A0031727molecular_functionCCR2 chemokine receptor binding
A0034351biological_processnegative regulation of glial cell apoptotic process
A0035684biological_processhelper T cell extravasation
A0043524biological_processnegative regulation of neuron apoptotic process
A0043615biological_processastrocyte cell migration
A0044344biological_processcellular response to fibroblast growth factor stimulus
A0048020molecular_functionCCR chemokine receptor binding
A0048245biological_processeosinophil chemotaxis
A0048246biological_processmacrophage chemotaxis
A0050870biological_processpositive regulation of T cell activation
A0051770biological_processpositive regulation of nitric-oxide synthase biosynthetic process
A0051968biological_processpositive regulation of synaptic transmission, glutamatergic
A0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
A0070098biological_processchemokine-mediated signaling pathway
A0071222biological_processcellular response to lipopolysaccharide
A0071346biological_processcellular response to type II interferon
A0071347biological_processcellular response to interleukin-1
A0071356biological_processcellular response to tumor necrosis factor
A0090280biological_processpositive regulation of calcium ion import
A1904783biological_processpositive regulation of NMDA glutamate receptor activity
A1905563biological_processnegative regulation of vascular endothelial cell proliferation
A2000134biological_processnegative regulation of G1/S transition of mitotic cell cycle
A2000353biological_processpositive regulation of endothelial cell apoptotic process
A2000427biological_processpositive regulation of apoptotic cell clearance
A2000502biological_processnegative regulation of natural killer cell chemotaxis
Functional Information from PDB Data
site_idAC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE 0U1 B 31
ChainResidue
B0A12
B0C13
B0G30
B0G32
BNA101
BHOH221
BHOH274
BHOH293

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA B 101
ChainResidue
BHOH221
BHOH245
BHOH246
BHOH248
B0U131

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SR B 102
ChainResidue
B0C9
B0C11
B0A12
BHOH206
BHOH213
BHOH215

site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE K B 103
ChainResidue
B0U6
BHOH230
BHOH256
BHOH283

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE K B 104
ChainResidue
B0U6
B0G18
BHOH273
BHOH276
BHOH285

site_idAC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE K B 105
ChainResidue
BHOH214
BHOH240
BHOH241
BHOH254
BHOH291

site_idAC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE K B 106
ChainResidue
B0G32
B0G33
BHOH235
BHOH236
BHOH271
BHOH272
BHOH296

site_idAC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE K B 107
ChainResidue
B0C13
BHOH229
BHOH292
BHOH293

Functional Information from PROSITE/UniProt
site_idPS00472
Number of Residues43
DetailsSMALL_CYTOKINES_CC Small cytokines (intercrine/chemokine) C-C subfamily signature. CCYnftnrk..IsvqrLasYrritssk.Cpke.AVIFktivakei.CA
ChainResidueDetails
ACYS11-ALA53

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues3
DetailsSITE: Involved in dimerization
ChainResidueDetails
APRO8
ALYS35
ALYS38

site_idSWS_FT_FI2
Number of Residues1
DetailsSITE: Involved in dimerization, receptor binding and signaling
ChainResidueDetails
ATYR13

site_idSWS_FT_FI3
Number of Residues4
DetailsSITE: Involved in GAG binding
ChainResidueDetails
AARG18
ALYS19
ALYS58
AHIS66

site_idSWS_FT_FI4
Number of Residues2
DetailsSITE: Involved in GAG binding and receptor binding
ChainResidueDetails
AARG24
ALYS49

site_idSWS_FT_FI5
Number of Residues1
DetailsMOD_RES: Pyrrolidone carboxylic acid => ECO:0000269|PubMed:1661560, ECO:0000269|PubMed:2648385
ChainResidueDetails
AGLN1

site_idSWS_FT_FI6
Number of Residues1
DetailsCARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000255
ChainResidueDetails
AASN14

222926

PDB entries from 2024-07-24

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