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- PDB-6m5e: Human serum albumin with cyclic peptide dalbavancin -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6m5e
TitleHuman serum albumin with cyclic peptide dalbavancin
Components
  • (dalbavancin) x 2
  • Serum albumin
KeywordsPEPTIDE BINDING PROTEIN / Transporter / Cyclic peptide
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin
Similarity search - Domain/homology
Chem-F8F / 2-amino-2-deoxy-beta-D-altropyranuronic acid / Chem-JEF / 10-METHYLUNDECANOIC ACID / alpha-D-mannopyranose / beta-L-allopyranose / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsIto, S. / Senoo, A. / Nagatoishi, S. / Ohue, M. / Yamamoto, M. / Tsumoto, K. / Wakui, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP19am0101001 (Support number 1851) Japan
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin.
Authors: Ito, S. / Senoo, A. / Nagatoishi, S. / Ohue, M. / Yamamoto, M. / Tsumoto, K. / Wakui, N.
History
DepositionMar 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Serum albumin
B: Serum albumin
C: Serum albumin
F: dalbavancin
G: dalbavancin
H: dalbavancin
I: dalbavancin
J: dalbavancin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,69529
Polymers206,2408
Non-polymers6,45521
Water543
1
A: Serum albumin
F: dalbavancin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6467
Polymers67,8762
Non-polymers1,7695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin
G: dalbavancin
J: dalbavancin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,52411
Polymers69,1823
Non-polymers2,3438
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serum albumin
H: dalbavancin
I: dalbavancin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,52411
Polymers69,1823
Non-polymers2,3438
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.050, 125.680, 125.740
Angle α, β, γ (deg.)90.000, 90.320, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 310 or (resid 311...
21(chain B and (resid 2 through 310 or (resid 311...
31(chain C and (resid 2 through 316 or (resid 317...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVAL(chain A and (resid 2 through 310 or (resid 311...AA2 - 3102 - 310
12GLUGLUGLUGLU(chain A and (resid 2 through 310 or (resid 311...AA311311
13ALAALAALAALA(chain A and (resid 2 through 310 or (resid 311...AA2 - 5822 - 582
14ALAALAALAALA(chain A and (resid 2 through 310 or (resid 311...AA2 - 5822 - 582
15ALAALAALAALA(chain A and (resid 2 through 310 or (resid 311...AA2 - 5822 - 582
16ALAALAALAALA(chain A and (resid 2 through 310 or (resid 311...AA2 - 5822 - 582
17ALAALAALAALA(chain A and (resid 2 through 310 or (resid 311...AA2 - 5822 - 582
18ALAALAALAALA(chain A and (resid 2 through 310 or (resid 311...AA2 - 5822 - 582
19ALAALAALAALA(chain A and (resid 2 through 310 or (resid 311...AA2 - 5822 - 582
21ALAALAVALVAL(chain B and (resid 2 through 310 or (resid 311...BB2 - 3102 - 310
22GLUGLUGLUGLU(chain B and (resid 2 through 310 or (resid 311...BB311311
23ALAALAALAALA(chain B and (resid 2 through 310 or (resid 311...BB2 - 5822 - 582
24ALAALAALAALA(chain B and (resid 2 through 310 or (resid 311...BB2 - 5822 - 582
25ALAALAALAALA(chain B and (resid 2 through 310 or (resid 311...BB2 - 5822 - 582
26ALAALAALAALA(chain B and (resid 2 through 310 or (resid 311...BB2 - 5822 - 582
27ALAALAALAALA(chain B and (resid 2 through 310 or (resid 311...BB2 - 5822 - 582
28ALAALAALAALA(chain B and (resid 2 through 310 or (resid 311...BB2 - 5822 - 582
29ALAALAALAALA(chain B and (resid 2 through 310 or (resid 311...BB2 - 5822 - 582
31ALAALACYSCYS(chain C and (resid 2 through 316 or (resid 317...CC2 - 3162 - 316
32LYSLYSLYSLYS(chain C and (resid 2 through 316 or (resid 317...CC317317
33ALAALAALAALA(chain C and (resid 2 through 316 or (resid 317...CC2 - 5822 - 582
34ALAALAALAALA(chain C and (resid 2 through 316 or (resid 317...CC2 - 5822 - 582
35ALAALAALAALA(chain C and (resid 2 through 316 or (resid 317...CC2 - 5822 - 582
36ALAALAALAALA(chain C and (resid 2 through 316 or (resid 317...CC2 - 5822 - 582

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Serum albumin /


Mass: 66571.219 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Homo sapiens (human) / References: UniProt: P02768

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Protein/peptide , 2 types, 5 molecules FGHIJ

#2: Protein/peptide dalbavancin /


Mass: 1305.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide dalbavancin /


Mass: 1305.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 3 types, 7 molecules

#7: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-F8X / 2-amino-2-deoxy-beta-D-altropyranuronic acid


Type: D-saccharide, beta linking / Mass: 193.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO6
#9: Sugar ChemComp-WOO / beta-L-allopyranose / beta-L-allose / L-allose / allose / Allose


Type: L-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
LAllpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-allopyranoseCOMMON NAMEGMML 1.0
b-L-AllpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AllSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 17 molecules

#4: Chemical
ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C30H63NO10
#5: Chemical ChemComp-F8F / (2S,5S)-5-azanyl-3,4,6-tris(oxidanyl)oxane-2-carboxylic acid


Mass: 193.155 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H11NO6
#6: Chemical
ChemComp-M12 / 10-METHYLUNDECANOIC ACID


Mass: 200.318 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H24O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0 30 % v/v Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.78 Å / Num. obs: 75497 / % possible obs: 100 % / Redundancy: 22.012 % / Biso Wilson estimate: 56.968 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.468 / Rrim(I) all: 0.479 / Χ2: 1.251 / Net I/σ(I): 9.27 / Num. measured all: 1661847 / Scaling rejects: 333
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.9721.4644.5611.0226084712153121530.5044.67100
2.97-3.1720.8072.2631.8223341111218112180.7282.319100
3.17-3.4321.941.1893.5523997810938109380.8921.217100
3.43-3.7623.2390.6546.7228560983598350.9610.668100
3.76-4.222.9480.37811.11202816883888380.9840.386100
4.2-4.8522.5260.24316.55176314782778270.9910.249100
4.85-5.9420.6240.22316.45137026664466440.9920.229100
5.94-8.422.3330.1621.89115641517851780.9970.164100
8.4-45.7823.4660.139.1667254288528660.9980.10299.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.3 Å49.26 Å
Translation4.3 Å49.26 Å

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ao6

1ao6


Resolution: 2.8→45.78 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 3775 5 %
Rwork0.1799 71702 -
obs0.1824 75477 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 232.32 Å2 / Biso mean: 66.0602 Å2 / Biso min: 21.25 Å2
Refinement stepCycle: final / Resolution: 2.8→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13840 0 1392 3 15235
Biso mean--93.58 57.04 -
Num. residues----1743
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8453X-RAY DIFFRACTION15.784TORSIONAL
12B8453X-RAY DIFFRACTION15.784TORSIONAL
13C8453X-RAY DIFFRACTION15.784TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.840.363980.306726672765100
2.84-2.870.35041340.288626482782100
2.87-2.910.33161320.268726852817100
2.91-2.950.29221410.25926062747100
2.95-30.27371320.257726792811100
3-3.040.36471420.282225972739100
3.04-3.090.32741360.275426412777100
3.09-3.150.29861420.255926822824100
3.15-3.210.30131410.23326302771100
3.21-3.270.30791370.224526432780100
3.27-3.330.31011250.226226732798100
3.33-3.410.28181190.209626542773100
3.41-3.490.25571180.20426922810100
3.49-3.570.24011360.19426392775100
3.57-3.670.23931130.183926782791100
3.67-3.780.21041160.172926802796100
3.78-3.90.2171440.162126632807100
3.9-4.040.20231520.157726402792100
4.04-4.20.20081670.144226492816100
4.2-4.390.20231620.13726002762100
4.39-4.620.17371380.129426632801100
4.62-4.910.17141600.127426412801100
4.91-5.290.17891580.138226492807100
5.29-5.820.23251390.163526722811100
5.82-6.660.23151450.185426792824100
6.66-8.380.20661730.163826682841100
8.38-45.780.18811750.14692684285999
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)
16.4396-3.4249-0.38312.67251.70326.085-0.19410.53570.1885-0.36670.03360.1718-0.449-0.20940.03750.5268-0.1244-0.06570.30840.08880.3357-59.268441.033425.2628
21.8802-0.4370.10282.10531.45832.2513-0.25240.06550.4464-0.27140.238-0.158-0.59060.1048-0.01340.5888-0.1388-0.0390.33270.03770.4666-47.013348.250436.3617
32.08090.92910.20491.1449-0.11051.07560.0765-0.2433-0.11210.09130.022-0.0849-0.0207-0.0843-0.10370.4137-0.05030.0270.2853-0.0190.2797-45.385126.511356.3999
45.44662.34-0.53674.5074-0.38173.293-0.09290.32070.3361-0.10750.1259-0.0062-0.35090.3378-0.03050.3606-0.05210.00920.3255-0.02330.2758-21.256446.335747.8145
55.07-0.03651.75884.8125-1.30214.6969-0.00020.2730.145-0.223-0.0731-0.0419-0.16740.06020.27520.28230.08690.02840.2557-0.01890.2778-26.122871.76672.0635
63.031-1.62371.82922.5808-1.80692.8590.18510.2698-0.1521-0.2568-0.15160.02770.11420.1998-0.07180.31360.07310.02410.3279-0.11870.3317-27.909761.600274.1356
72.227-0.1655-0.41492.2690.19681.9301-0.1869-0.2140.0320.32220.28210.04050.02880.0005-0.12330.45250.18590.00920.34060.00440.2964-43.181176.764396.6658
82.2424-0.71080.41893.56990.42562.3316-0.068-0.2237-0.70160.65240.26070.28730.8937-0.0042-0.17240.79520.07540.07570.45480.09620.6883-50.358352.80199.2954
92.5217-0.55830.09473.70540.01012.06460.03920.549-0.4003-0.02010.0780.3231.14870.2168-0.08740.81070.0898-0.00740.5309-0.09140.6647-50.369347.910187.7109
10-0.0036-0.07650.00041.5856-0.0341-0.0024-0.29920.0901-0.795-0.30970.3975-0.1621.24130.3447-0.14271.89430.3194-0.18460.9181-0.22461.4588-44.714727.219790.146
112.8660.67-1.35871.5672-0.4372.6987-0.00220.3095-0.0709-0.01610.05420.11980.1919-0.4701-0.05480.2618-0.0695-0.07030.38130.01060.2941-25.396835.2684115.7832
121.6297-0.81820.23421.1811-0.24671.2150.0003-0.29790.0223-0.05120.10040.2078-0.1116-0.3613-0.07950.262-0.0029-0.00170.42490.03330.3003-22.945154.2974136.6135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 81 )A2 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 206 )A82 - 206
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 414 )A207 - 414
4X-RAY DIFFRACTION4chain 'A' and (resid 415 through 582 )A415 - 582
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 35 )B2 - 35
6X-RAY DIFFRACTION6chain 'B' and (resid 36 through 206 )B36 - 206
7X-RAY DIFFRACTION7chain 'B' and (resid 207 through 365 )B207 - 365
8X-RAY DIFFRACTION8chain 'B' and (resid 366 through 441 )B366 - 441
9X-RAY DIFFRACTION9chain 'B' and (resid 442 through 517 )B442 - 517
10X-RAY DIFFRACTION10chain 'B' and (resid 518 through 582 )B518 - 582
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 206 )C2 - 206
12X-RAY DIFFRACTION12chain 'C' and (resid 207 through 582 )C207 - 582

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