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- PDB-5fv9: Crystal structure of GalNAc-T2 in complex with compound 16d -

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Basic information

Entry
Database: PDB / ID: 5fv9
TitleCrystal structure of GalNAc-T2 in complex with compound 16d
ComponentsGALNAC-T2
KeywordsTRANSFERASE
Function / homology
Function and homology information


: / : / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / O-linked glycosylation of mucins / protein O-linked glycosylation / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / Golgi cisterna membrane ...: / : / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / O-linked glycosylation of mucins / protein O-linked glycosylation / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / Golgi cisterna membrane / positive regulation of immunoglobulin production / protein maturation / manganese ion binding / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular region / membrane
Similarity search - Function
N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A ...N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / Chem-Y6W / Polypeptide N-acetylgalactosaminyltransferase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsGhirardello, M. / Rivas, M. / Lacetera, A. / Delso, I. / Lira-Navarrete, E. / Tejero, T. / Martin-Santamaria, S. / Hurtado-Guerrero, R. / Merino, P.
CitationJournal: Chemistry / Year: 2016
Title: Glycomimetics Targeting Glycosyltransferases: Synthetic, Computational and Structural Studies of Less-Polar Conjugates.
Authors: Ghirardello, M. / De Las Rivas, M. / Lacetera, A. / Delso, I. / Lira-Navarrete, E. / Tejero, T. / Martin-Santamaria, S. / Hurtado-Guerrero, R. / Merino, P.
History
DepositionFeb 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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 / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GALNAC-T2
B: GALNAC-T2
C: GALNAC-T2
D: GALNAC-T2
E: GALNAC-T2
F: GALNAC-T2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,56940
Polymers388,9486
Non-polymers5,62134
Water29,4181633
1
C: GALNAC-T2
D: GALNAC-T2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7849
Polymers129,6492
Non-polymers1,1347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-39.1 kcal/mol
Surface area39060 Å2
MethodPISA
2
A: GALNAC-T2
B: GALNAC-T2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,57514
Polymers129,6492
Non-polymers1,92512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-26.7 kcal/mol
Surface area39760 Å2
MethodPISA
3
F: GALNAC-T2
hetero molecules

E: GALNAC-T2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,21117
Polymers129,6492
Non-polymers2,56215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5660 Å2
ΔGint-22.2 kcal/mol
Surface area39660 Å2
MethodPISA
4
E: GALNAC-T2
hetero molecules

F: GALNAC-T2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,21117
Polymers129,6492
Non-polymers2,56215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area5660 Å2
ΔGint-22.2 kcal/mol
Surface area39660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.493, 121.748, 250.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.05266, 0.9073, -0.4171), (0.8821, -0.1536, -0.4454), (-0.4682, -0.3914, -0.7922)
Vector: 41.04, -63.38, -39.74)

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
GALNAC-T2


Mass: 64824.703 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZALPHAA / Production host: KOMAGATAELLA PASTORIS (fungus) / Variant (production host): X33 / References: UniProt: Q10471

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Non-polymers , 6 types, 1667 molecules

#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-Y6W / [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl hydrogen (S)-{3-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]propyl}phosphonate


Mass: 512.402 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H29N2O13P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1633 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.06 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.07→20 Å / Num. obs: 215817 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shellResolution: 2.07→2.12 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DOT

4dot


Resolution: 2.07→250.15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 10.755 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24685 5938 2.8 %RANDOM
Rwork0.18958 ---
obs0.19113 209784 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.18 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.07→250.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22937 0 344 1633 24914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01923798
X-RAY DIFFRACTIONr_bond_other_d0.0020.0222481
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.95932211
X-RAY DIFFRACTIONr_angle_other_deg1.0213.00251532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72252860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6823.2711171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.302154057
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5315231
X-RAY DIFFRACTIONr_chiral_restr0.1480.23426
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02126853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025743
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_it2.893.15211458
X-RAY DIFFRACTIONr_mcbond_other2.8893.15211457
X-RAY DIFFRACTIONr_mcangle_it4.1814.70814309
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4733.58312340
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: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 460 -
Rwork0.269 15402 -
obs--99.84 %
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)
10.2008-0.24720.01120.5102-0.10360.12710.0761-0.06110.0199-0.0735-0.0623-0.0197-0.01440.0009-0.01380.098-0.03510.00690.14940.0150.084630.0625-1.5823-55.3867
20.10720.15960.00240.41740.24810.39810.0248-0.02730.0017-0.008-0.05040.0567-0.0524-0.00850.02560.0962-0.01540.02350.18840.0030.075910.1393-39.8047-37.8523
30.3597-0.2545-0.52410.2390.34510.8405-0.076-0.02240.00530.10330.0925-0.00550.03560.0842-0.01650.1370.03490.01620.2421-0.00390.005121.5476-32.40170.8822
40.27250.1153-0.30280.5713-0.8441.3368-0.15540.0377-0.03080.05780.1044-0.0439-0.0228-0.1770.0510.147-0.01790.02530.14390.03890.0429-15.287428.6427-19.2237
50.1102-0.23660.240.5606-0.63090.9955-0.13780.02220.08430.2456-0.0446-0.1972-0.23650.00530.18240.21710.019-0.08840.15790.00450.0759-3.68319.649720.244
61.2445-0.6109-0.32890.51770.39760.34330.3393-0.21280.2862-0.1631-0.0574-0.3179-0.0768-0.1013-0.2820.2304-0.08330.15810.13430.05920.2679-49.294-9.4242-43.4098
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E75 - 602
2X-RAY DIFFRACTION2A75 - 601
3X-RAY DIFFRACTION3B75 - 602
4X-RAY DIFFRACTION4C75 - 601
5X-RAY DIFFRACTION5D75 - 601
6X-RAY DIFFRACTION6F75 - 602

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