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- PDB-4uai: Crystal structure of CXCL12 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 4uai
TitleCrystal structure of CXCL12 in complex with inhibitor
ComponentsStromal cell-derived factor 1
KeywordsCYTOKINE/CYTOKINE INHIBITOR / CXCL12 / inhibitor / complex / chemokine / CYTOKINE-CYTOKINE INHIBITOR complex
Function / homology
Function and homology information


chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance ...chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of dopamine secretion / Signaling by ROBO receptors / induction of positive chemotaxis / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / chemokine-mediated signaling pathway / blood circulation / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / positive regulation of calcium ion import / detection of temperature stimulus involved in sensory perception of pain / positive regulation of cell adhesion / positive regulation of T cell migration / animal organ regeneration / Nuclear signaling by ERBB4 / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / cell chemotaxis / adult locomotory behavior / axon guidance / neuron migration / response to virus / growth factor activity / defense response / intracellular calcium ion homeostasis / response to peptide hormone / chemotaxis / integrin binding / G alpha (i) signalling events / collagen-containing extracellular matrix / Estrogen-dependent gene expression / response to hypoxia / cell adhesion / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / signal transduction / extracellular exosome / extracellular region
Similarity search - Function
Stromal cell-derived factor 1 / CXC Chemokine domain / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
1-phenyl-3-[4-(1H-tetrazol-5-yl)phenyl]urea / Stromal cell-derived factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSmith, E.W. / Chen, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097381 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI058072 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA173056 United States
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structural Analysis of a Novel Small Molecule Ligand Bound to the CXCL12 Chemokine.
Authors: Smith, E.W. / Liu, Y. / Getschman, A.E. / Peterson, F.C. / Ziarek, J.J. / Li, R. / Volkman, B.F. / Chen, Y.
History
DepositionAug 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 2.0Sep 27, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site_anisotrop / citation ...atom_site_anisotrop / citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 2.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stromal cell-derived factor 1
B: Stromal cell-derived factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4295
Polymers15,9572
Non-polymers4723
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-31 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.930, 57.710, 72.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 2 - 67 / Label seq-ID: 2 - 67

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Stromal cell-derived factor 1 / / hSDF-1 / C-X-C motif chemokine 12 / Intercrine reduced in hepatomas / hIRH / Pre-B cell growth- ...hSDF-1 / C-X-C motif chemokine 12 / Intercrine reduced in hepatomas / hIRH / Pre-B cell growth-stimulating factor / PBSF


Mass: 7978.460 Da / Num. of mol.: 2 / Fragment: UNP residues 22-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1, SDF1A, SDF1B / Production host: Escherichia coli (E. coli) / References: UniProt: P48061
#2: Chemical ChemComp-3GG / 1-phenyl-3-[4-(1H-tetrazol-5-yl)phenyl]urea


Mass: 280.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N6O
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2 M AmSO4, 2% MPD, 0.1 M MES Sodium Salt pH 6.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→45.16 Å / Num. obs: 12099 / % possible obs: 99.8 % / Redundancy: 6.89 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.77

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0073refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J7Z

2j7z


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.465 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 637 5 %RANDOM
Rwork0.1863 ---
obs-12099 99.8 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.111 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0 Å2
2--0.12 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 31 40 1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191164
X-RAY DIFFRACTIONr_bond_other_d0.0050.021164
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.9861572
X-RAY DIFFRACTIONr_angle_other_deg1.37532664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5545133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.823.46252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82715218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7471510
X-RAY DIFFRACTIONr_chiral_restr0.1080.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211271
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02281
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0671.832538
X-RAY DIFFRACTIONr_mcbond_other3.0291.825537
X-RAY DIFFRACTIONr_mcangle_it4.0192.706669
X-RAY DIFFRACTIONr_mcangle_other4.032.713670
X-RAY DIFFRACTIONr_scbond_it5.6722.658626
X-RAY DIFFRACTIONr_scbond_other5.3052.62618
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4633.639892
X-RAY DIFFRACTIONr_long_range_B_refined9.62116.4491238
X-RAY DIFFRACTIONr_long_range_B_other9.61916.4831239
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3472 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 47 -
Rwork0.215 889 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.21620.9673-0.20071.9092-0.44971.7908-0.03720.0557-0.1383-0.05660.0211-0.0160.05090.02060.01610.0720.02860.01240.0165-0.00680.0367.758-8.0889.941
23.1369-0.28710.15366.00010.20814.17210.0062-0.00580.00680.0020.00940.2174-0.0798-0.1049-0.01570.0587-0.01660.00930.0369-0.01650.02326.2172.19220.039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 68
2X-RAY DIFFRACTION2B2 - 68

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