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- PDB-4d69: SOYBEAN AGGLUTININ FROM GLYCINE MAX IN COMPLEX WITH THE ANTIGEN Tn -

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Basic information

Entry
Database: PDB / ID: 4d69
TitleSOYBEAN AGGLUTININ FROM GLYCINE MAX IN COMPLEX WITH THE ANTIGEN Tn
Components
  • LECTIN
  • SHORT ANTIGEN PEPTIDE
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / : / Lectin
Similarity search - Component
Biological speciesGLYCINE MAX (soybean)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMadariaga, D. / Martinez-Saez, N. / Somovilla, V.J. / Coelho, H. / Valero-Gonzalez, J. / Castro-Lopez, J. / Asensio, J.L. / Jimenez-Barbero, J. / Busto, J.H. / Avenoza, A. ...Madariaga, D. / Martinez-Saez, N. / Somovilla, V.J. / Coelho, H. / Valero-Gonzalez, J. / Castro-Lopez, J. / Asensio, J.L. / Jimenez-Barbero, J. / Busto, J.H. / Avenoza, A. / Marcelo, F. / Hurtado-Guerrero, R. / Corzana, F. / Peregrina, J.M.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Detection of Tumor-Associated Glycopeptides by Lectins: The Peptide Context Modulates Carbohydrate Recognition.
Authors: Madariaga, D. / Martinez-Saez, N. / Somovilla, V.J. / Coelho, H. / Valero-Gonzalez, J. / Castro-Lopez, J. / Asensio, J.L. / Jimenez-Barbero, J. / Busto, J.H. / Avenoza, A. / Marcelo, F. / ...Authors: Madariaga, D. / Martinez-Saez, N. / Somovilla, V.J. / Coelho, H. / Valero-Gonzalez, J. / Castro-Lopez, J. / Asensio, J.L. / Jimenez-Barbero, J. / Busto, J.H. / Avenoza, A. / Marcelo, F. / Hurtado-Guerrero, R. / Corzana, F. / Peregrina, J.M.
History
DepositionNov 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LECTIN
B: LECTIN
C: LECTIN
D: LECTIN
E: LECTIN
F: LECTIN
G: LECTIN
H: LECTIN
I: LECTIN
J: LECTIN
K: LECTIN
L: LECTIN
O: SHORT ANTIGEN PEPTIDE
P: SHORT ANTIGEN PEPTIDE
Q: SHORT ANTIGEN PEPTIDE
R: SHORT ANTIGEN PEPTIDE
S: SHORT ANTIGEN PEPTIDE
T: SHORT ANTIGEN PEPTIDE
U: SHORT ANTIGEN PEPTIDE
V: SHORT ANTIGEN PEPTIDE
W: SHORT ANTIGEN PEPTIDE
X: SHORT ANTIGEN PEPTIDE
Y: SHORT ANTIGEN PEPTIDE
Z: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,93172
Polymers337,86524
Non-polymers9,06648
Water2,126118
1
I: LECTIN
O: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: LECTIN
P: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
J: LECTIN
Q: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: LECTIN
R: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: LECTIN
S: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: LECTIN
T: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
E: LECTIN
U: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
L: LECTIN
V: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
G: LECTIN
W: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
F: LECTIN
X: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: LECTIN
Y: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
H: LECTIN
Z: SHORT ANTIGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9116
Polymers28,1552
Non-polymers7554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.232, 114.232, 202.893
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6846, 0.7284, -0.02835), (0.7289, -0.6836, 0.03711), (0.007651, -0.04606, -0.9989)
Vector: 106.2, -76.25, 22.93)

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Components

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Protein / Protein/peptide , 2 types, 24 molecules ABCDEFGHIJKLOPQRSTUVWXYZ

#1: Protein
LECTIN / / AGGLUTININ / SBA / SOYBEAN AGGLUTININ FROM GLYCINE MAX


Mass: 27595.816 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) GLYCINE MAX (soybean) / References: UniProt: P05046
#2: Protein/peptide
SHORT ANTIGEN PEPTIDE


Mass: 559.593 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others)

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Sugars , 2 types, 24 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 142 molecules

#5: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.54 % / Description: NONE

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 81148 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SBF

1sbf


Resolution: 2.7→202.89 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.899 / SU B: 37.493 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27433 2232 2.8 %RANDOM
Rwork0.23022 ---
obs0.23146 78876 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.993 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20.76 Å20 Å2
2--1.52 Å20 Å2
3----4.94 Å2
Refinement stepCycle: LAST / Resolution: 2.7→202.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21854 0 528 118 22500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01923078
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221304
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.96731563
X-RAY DIFFRACTIONr_angle_other_deg0.816349085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.45452818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50124.808965
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.045153461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9441577
X-RAY DIFFRACTIONr_chiral_restr0.0840.23668
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02125811
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025164
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_it1.0760.62611332
X-RAY DIFFRACTIONr_mcbond_other1.0680.62611331
X-RAY DIFFRACTIONr_mcangle_it1.9090.92114124
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3080.84511746
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 153 -
Rwork0.358 5843 -
obs--99.98 %
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)
12.3933-0.77630.6930.2995-0.25990.74330.45870.7983-0.1226-0.0247-0.30780.0760.23960.3485-0.15090.51560.1539-0.00490.6603-0.13670.692866.9517-46.56036.7467
20.3605-0.4259-0.1641.09140.47492.7548-0.17320.0958-0.050.3756-0.00150.2134-0.14830.16740.17470.7441-0.00160.10260.3188-0.02520.5765-5.3083-48.069518.5159
30.2055-0.1980.21250.25640.0741.6602-0.0893-0.0745-0.0457-0.00010.14050.0675-0.17570.4711-0.05120.3939-0.1491-0.050.78430.14220.612819.0927-70.1412-48.3149
40.3451-0.1159-0.52481.4165-0.22381.113-0.0795-0.01780.0634-0.1145-0.126-0.19820.275-0.03420.20550.5554-0.01370.03760.40780.02290.68124.8871-18.4086-29.6244
51.14-0.14420.68940.87420.30461.15880.15270.17560.0516-0.0092-0.25520.0577-0.0129-0.07320.10250.39630.00370.01440.5426-0.04430.679837.7768-30.57657.3425
60.16890.17070.25971.51490.24261.01340.11620.12970.03080.3165-0.07340.2419-0.1240.0785-0.04270.5203-0.00680.12020.39170.01960.732453.4081-17.9056-25.1224
71.0415-0.003-0.71341.31340.16221.1552-0.13290.14090.00520.3623-0.14210.28110.35650.08750.2750.5328-0.03170.15880.3608-0.00720.765347.7493-50.5656-26.9343
80.4933-0.11210.23741.0389-0.57031.59420.0020.0003-0.0071-0.0542-0.0831-0.1657-0.4010.04270.0810.6059-0.0571-0.02560.36960.03230.692861.2067-84.2178-33.1248
90.3966-0.1119-0.35132.4540.78040.5843-0.16030.0692-0.01280.18510.06060.14260.24720.08730.09970.6342-0.00490.07050.3889-0.00790.6013.0682-84.7808-13.9498
100.13660.3731-0.29781.7055-0.68692.3570.24650.0841-0.07981.1394-0.1688-0.0241-0.9375-0.1167-0.07771.3338-0.0696-0.02250.2771-0.06350.559950.7868-81.13882.7857
110.2598-0.3799-0.20121.56510.44911.16620.0789-0.1762-0.0454-0.35430.0170.0455-0.2630.1023-0.09590.6565-0.05090.0290.3753-0.00780.60895.1731-51.9231-17.2033
120.66060.3777-0.00511.006-0.05041.45850.18050.17350.08280.5117-0.22770.01280.267-0.13750.04720.7942-0.15860.04010.3331-0.05070.5637-11.6548-15.12233.6181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 234
2X-RAY DIFFRACTION2B1 - 233
3X-RAY DIFFRACTION3C1 - 234
4X-RAY DIFFRACTION4D1 - 234
5X-RAY DIFFRACTION5E1 - 234
6X-RAY DIFFRACTION6F1 - 234
7X-RAY DIFFRACTION7G1 - 234
8X-RAY DIFFRACTION8H1 - 234
9X-RAY DIFFRACTION9I1 - 234
10X-RAY DIFFRACTION10J1 - 234
11X-RAY DIFFRACTION11K1 - 234
12X-RAY DIFFRACTION12L1 - 234

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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