PDB Short entry for 2MK7 HEADER STRUCTURAL PROTEIN 02-FEB-14 2MK7 TITLE TETRA-O-GALNAC GLYCOSYLATED MUCIN SEQUENCE FROM ALPHA DYSTROGLYCAN TITLE 2 MUCIN DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-DYSTROGLYCAN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MUCIN DOMAIN PEPTIDE (UNP RESIDUES 419-427); COMPND 5 SYNONYM: ALPHA-DG, ADG; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS MUCIN DOMAIN, GLYCOPROTEIN, GLYCOSYLATION, ALPHA-DYSTROGLYCAN, TN KEYWDS 2 ANTIGEN, N-ACETYL-GALACTOSAMINE, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR D.LIVE,A.BORGERT REVDAT 4 14-JUN-23 2MK7 1 REMARK REVDAT 3 24-AUG-22 2MK7 1 JRNL HETSYN REVDAT 2 29-JUL-20 2MK7 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 LINK SITE ATOM REVDAT 1 04-FEB-15 2MK7 0 JRNL AUTH A.BORGERT,B.L.FOLEY,D.LIVE JRNL TITL CONTRASTING THE CONFORMATIONAL EFFECTS OF ALPHA-O-GALNAC AND JRNL TITL 2 ALPHA-O-MAN GLYCAN PROTEIN MODIFICATIONS AND THEIR IMPACT ON JRNL TITL 3 THE MUCIN-LIKE REGION OF ALPHA-DYSTROGLYCAN. JRNL REF GLYCOBIOLOGY V. 31 649 2021 JRNL REFN ESSN 1460-2423 JRNL PMID 33295623 JRNL DOI 10.1093/GLYCOB/CWAA112 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MK7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000103712. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2-10 MM ADG MUCIN DOMAIN REMARK 210 PEPTIDE, 100% D2O; 2-10 MM ADG REMARK 210 MUCIN DOMAIN PEPTIDE, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 3D TOCSY-NOESY; REMARK 210 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H COSY; REMARK 210 2D 1H-13C HMBC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 2 PRO A 3 165.65 -44.57 REMARK 500 3 PRO A 3 91.55 -44.52 REMARK 500 3 LYS A 9 74.08 19.98 REMARK 500 4 PRO A 3 163.29 -44.49 REMARK 500 5 PRO A 3 105.17 -44.56 REMARK 500 5 LYS A 8 96.21 42.91 REMARK 500 7 PRO A 3 150.99 -44.63 REMARK 500 7 LYS A 9 46.65 -175.82 REMARK 500 8 PRO A 3 151.21 -42.29 REMARK 500 9 PRO A 3 156.73 -42.59 REMARK 500 10 PRO A 3 155.02 -43.98 REMARK 500 10 LYS A 9 46.55 -175.86 REMARK 500 11 PRO A 3 95.82 -44.59 REMARK 500 11 LYS A 8 -146.92 46.42 REMARK 500 11 LYS A 9 61.31 21.39 REMARK 500 12 PRO A 3 91.53 -44.61 REMARK 500 12 LYS A 8 -176.98 47.36 REMARK 500 12 LYS A 9 46.44 -176.72 REMARK 500 13 PRO A 3 98.87 -46.37 REMARK 500 14 PRO A 3 155.71 -44.26 REMARK 500 14 LYS A 8 166.21 73.08 REMARK 500 15 LYS A 9 74.12 19.94 REMARK 500 16 LYS A 9 61.22 21.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19759 RELATED DB: BMRB DBREF 2MK7 A 2 10 UNP Q14118 DAG1_HUMAN 419 427 SEQADV 2MK7 ACE A 1 UNP Q14118 ACETYLATION SEQADV 2MK7 NH2 A 11 UNP Q14118 AMIDATION SEQRES 1 A 11 ACE PRO PRO THR THR THR THR LYS LYS PRO NH2 MODRES 2MK7 THR A 5 THR GLYCOSYLATION SITE MODRES 2MK7 THR A 7 THR GLYCOSYLATION SITE MODRES 2MK7 THR A 6 THR GLYCOSYLATION SITE MODRES 2MK7 THR A 4 THR GLYCOSYLATION SITE HET ACE A 1 6 HET NH2 A 11 3 HET A2G A 101 28 HET A2G A 102 28 HET A2G A 103 28 HET A2G A 104 28 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE FORMUL 1 ACE C2 H4 O FORMUL 1 NH2 H2 N FORMUL 2 A2G 4(C8 H15 N O6) LINK C ACE A 1 N PRO A 2 1555 1555 1.31 LINK OG1 THR A 4 C1 A2G A 101 1555 1555 1.41 LINK OG1 THR A 5 C1 A2G A 102 1555 1555 1.41 LINK OG1 THR A 6 C1 A2G A 103 1555 1555 1.41 LINK OG1 THR A 7 C1 A2G A 104 1555 1555 1.41 LINK C PRO A 10 N NH2 A 11 1555 1555 1.31 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000