PDB Short entry for 5ZGG HEADER MEMBRANE PROTEIN 08-MAR-18 5ZGG TITLE NMR STRUCTURE OF P75NTR TRANSMEMBRANE DOMAIN IN COMPLEX WITH NSC49652 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 16; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: P75NTR TMD, GP80-LNGFR,LOW AFFINITY NEUROTROPHIN RECEPTOR COMPND 5 P75NTR,LOW-AFFINITY NERVE GROWTH FACTOR RECEPTOR,NGF RECEPTOR,P75 COMPND 6 ICD; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NGFR, TNFRSF16; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SOLUBL21 KEYWDS TRANSMEMBRANE, COMPLEX, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Z.LIN,C.IBANEZ REVDAT 2 25-SEP-19 5ZGG 1 JRNL REMARK REVDAT 1 13-MAR-19 5ZGG 0 JRNL AUTH E.T.H.GOH,Z.LIN,B.Y.AHN,V.LOPES-RODRIGUES,N.H.DANG,S.SALIM, JRNL AUTH 2 B.BERGER,B.DYMOCK,D.L.SENGER,C.F.IBANEZ JRNL TITL A SMALL MOLECULE TARGETING THE TRANSMEMBRANE DOMAIN OF DEATH JRNL TITL 2 RECEPTOR P75NTRINDUCES MELANOMA CELL DEATH AND REDUCES TUMOR JRNL TITL 3 GROWTH. JRNL REF CELL CHEM BIOL V. 25 1485 2018 JRNL REFN ESSN 2451-9456 JRNL PMID 30293939 JRNL DOI 10.1016/J.CHEMBIOL.2018.09.007 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5ZGG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300006967. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 P75NTR TMD, 3.9 MM 4809F6, 100 REMARK 210 MM [U-98% 2H] DPC, 5 % [U-99.9% REMARK 210 2H] DMSO, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HCCH-TOCSY; 2D TOCSY; 3D REMARK 210 NOESY; 2D 1H-13C FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, CYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1 THR A 248 -45.92 -140.24 REMARK 500 1 THR B 248 -42.58 -141.39 REMARK 500 1 LEU B 251 25.73 -74.72 REMARK 500 2 THR A 248 -37.09 -140.94 REMARK 500 2 THR B 248 -39.47 -156.46 REMARK 500 3 THR A 248 -44.95 -139.81 REMARK 500 3 THR B 248 -40.46 -140.18 REMARK 500 3 LEU B 251 27.63 -76.16 REMARK 500 4 THR A 248 -37.48 -146.11 REMARK 500 4 THR B 248 -35.95 -150.98 REMARK 500 5 THR A 248 -44.56 -139.61 REMARK 500 5 LEU A 251 20.97 -77.36 REMARK 500 5 THR B 248 -38.25 -145.09 REMARK 500 6 THR A 248 -41.33 -141.94 REMARK 500 6 THR B 248 -38.90 -149.26 REMARK 500 6 LEU B 251 24.42 -74.72 REMARK 500 7 THR A 248 -44.17 -142.35 REMARK 500 7 THR B 247 56.87 -146.81 REMARK 500 7 THR B 248 -41.29 -149.98 REMARK 500 7 LEU B 251 29.22 -76.12 REMARK 500 8 THR A 248 -36.58 -146.52 REMARK 500 8 LEU B 251 25.35 -79.32 REMARK 500 9 THR A 248 -38.71 -146.70 REMARK 500 9 THR B 248 -42.42 -145.56 REMARK 500 10 THR A 248 -38.11 -142.86 REMARK 500 10 THR B 248 -45.05 -133.22 REMARK 500 10 LEU B 251 20.05 -56.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9F6 B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36172 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF P75NTR TRANSMEMBRANE DOMAIN IN COMPLEX WITH 4809F6 DBREF 5ZGG A 244 277 UNP P08138 TNR16_HUMAN 244 277 DBREF 5ZGG B 244 277 UNP P08138 TNR16_HUMAN 244 277 SEQRES 1 A 34 THR ARG GLY THR THR ASP ASN LEU ILE PRO VAL TYR CYS SEQRES 2 A 34 SER ILE LEU ALA ALA VAL VAL VAL GLY LEU VAL ALA TYR SEQRES 3 A 34 ILE ALA PHE LYS ARG TRP ASN SER SEQRES 1 B 34 THR ARG GLY THR THR ASP ASN LEU ILE PRO VAL TYR CYS SEQRES 2 B 34 SER ILE LEU ALA ALA VAL VAL VAL GLY LEU VAL ALA TYR SEQRES 3 B 34 ILE ALA PHE LYS ARG TRP ASN SER HET 9F6 B 301 27 HETNAM 9F6 (2E)-1-(2-HYDROXYPHENYL)-3-(PYRIDIN-3-YL)PROP-2-EN-1- HETNAM 2 9F6 ONE FORMUL 3 9F6 C14 H11 N O2 HELIX 1 AA1 LEU A 251 SER A 277 1 27 HELIX 2 AA2 LEU B 251 SER B 277 1 27 SSBOND 1 CYS A 256 CYS B 256 1555 1555 2.02 SITE 1 AC1 4 PRO A 253 ILE B 252 PRO B 253 CYS B 256 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