HEADER T-CELL SURFACE GLYCOPROTEIN 26-JAN-94 1CDI TITLE STRUCTURES OF AN HIV AND MHC BINDING FRAGMENT FROM HUMAN CD4 AS TITLE 2 REFINED IN TWO CRYSTAL LATTICES COMPND MOL_ID: 1; COMPND 2 MOLECULE: T CELL SURFACE GLYCOPROTEIN CD4; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS T-CELL SURFACE GLYCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.E.RYU,A.TRUNEH,R.W.SWEET,W.A.HENDRICKSON REVDAT 5 14-AUG-19 1CDI 1 REMARK REVDAT 4 17-JUL-19 1CDI 1 REMARK REVDAT 3 24-FEB-09 1CDI 1 VERSN REVDAT 2 01-APR-03 1CDI 1 JRNL REVDAT 1 30-APR-94 1CDI 0 JRNL AUTH S.E.RYU,A.TRUNEH,R.W.SWEET,W.A.HENDRICKSON JRNL TITL STRUCTURES OF AN HIV AND MHC BINDING FRAGMENT FROM HUMAN CD4 JRNL TITL 2 AS REFINED IN TWO CRYSTAL LATTICES. JRNL REF STRUCTURE V. 2 59 1994 JRNL REFN ISSN 0969-2126 JRNL PMID 8075984 JRNL DOI 10.1016/S0969-2126(00)00008-3 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 3235 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1390 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.440 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.796 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.545 ; 1.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.910 ; 2.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CDI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 66.77500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.13500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 66.77500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.13500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 118.81527 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 137.42231 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N GLN A 40 O PHE A 43 2.00 REMARK 500 O ASN A 164 N LYS A 166 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 1 CA - CB - CG ANGL. DEV. = 13.4 DEGREES REMARK 500 GLN A 20 N - CA - CB ANGL. DEV. = 15.2 DEGREES REMARK 500 GLN A 20 CA - CB - CG ANGL. DEV. = 23.4 DEGREES REMARK 500 THR A 45 N - CA - CB ANGL. DEV. = 14.7 DEGREES REMARK 500 ASP A 56 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 58 CD - NE - CZ ANGL. DEV. = 16.4 DEGREES REMARK 500 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 THR A 81 N - CA - CB ANGL. DEV. = 16.1 DEGREES REMARK 500 LEU A 95 N - CA - CB ANGL. DEV. = -12.9 DEGREES REMARK 500 ARG A 134 CD - NE - CZ ANGL. DEV. = 16.7 DEGREES REMARK 500 ARG A 134 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 1 92.62 -46.37 REMARK 500 ALA A 18 -82.75 -86.12 REMARK 500 SER A 19 21.99 85.71 REMARK 500 LYS A 21 128.06 -30.21 REMARK 500 SER A 31 -35.74 -37.10 REMARK 500 ASN A 32 22.59 -64.04 REMARK 500 GLN A 33 -17.75 53.18 REMARK 500 SER A 49 154.16 176.12 REMARK 500 SER A 60 -44.14 -28.97 REMARK 500 ASN A 73 71.70 38.08 REMARK 500 ASP A 78 8.14 -57.34 REMARK 500 GLU A 87 -77.00 35.73 REMARK 500 ASN A 103 8.42 -53.04 REMARK 500 SER A 104 -87.00 -111.77 REMARK 500 ASP A 105 -157.49 173.02 REMARK 500 SER A 125 60.51 -116.85 REMARK 500 ILE A 138 101.08 -169.21 REMARK 500 LEU A 151 -58.52 30.02 REMARK 500 ASP A 153 37.92 -88.70 REMARK 500 GLN A 163 -108.43 -117.48 REMARK 500 GLN A 165 -73.11 54.14 REMARK 500 REMARK 500 REMARK: NULL DBREF 1CDI A 0 178 UNP P01730 CD4_HUMAN 23 203 SEQADV 1CDI THR A 0 UNP P01730 GLY 25 CONFLICT SEQRES 1 A 179 THR LYS LYS VAL VAL LEU GLY LYS LYS GLY ASP THR VAL SEQRES 2 A 179 GLU LEU THR CYS THR ALA SER GLN LYS LYS SER ILE GLN SEQRES 3 A 179 PHE HIS TRP LYS ASN SER ASN GLN ILE LYS ILE LEU GLY SEQRES 4 A 179 ASN GLN GLY SER PHE LEU THR LYS GLY PRO SER LYS LEU SEQRES 5 A 179 ASN ASP ARG ALA ASP SER ARG ARG SER LEU TRP ASP GLN SEQRES 6 A 179 GLY ASN PHE PRO LEU ILE ILE LYS ASN LEU LYS ILE GLU SEQRES 7 A 179 ASP SER ASP THR TYR ILE CYS GLU VAL GLU ASP GLN LYS SEQRES 8 A 179 GLU GLU VAL GLN LEU LEU VAL PHE GLY LEU THR ALA ASN SEQRES 9 A 179 SER ASP THR HIS LEU LEU GLN GLY GLN SER LEU THR LEU SEQRES 10 A 179 THR LEU GLU SER PRO PRO GLY SER SER PRO SER VAL GLN SEQRES 11 A 179 CYS ARG SER PRO ARG GLY LYS ASN ILE GLN GLY GLY LYS SEQRES 12 A 179 THR LEU SER VAL SER GLN LEU GLU LEU GLN ASP SER GLY SEQRES 13 A 179 THR TRP THR CYS THR VAL LEU GLN ASN GLN LYS LYS VAL SEQRES 14 A 179 GLU PHE LYS ILE ASP ILE VAL VAL LEU ALA HELIX 1 1 ARG A 58 GLY A 65 5 8 HELIX 2 2 LYS A 75 SER A 79 5 5 HELIX 3 3 GLU A 150 SER A 154 5 5 SHEET 1 D1A 3 ARG A 54 ARG A 58 0 SHEET 2 D1A 3 GLN A 64 LYS A 72 -1 SHEET 3 D1A 3 VAL A 12 ALA A 18 -1 SHEET 1 D1B 6 LYS A 2 LYS A 8 0 SHEET 2 D1B 6 GLN A 89 PHE A 98 1 SHEET 3 D1B 6 ASP A 80 VAL A 86 -1 SHEET 4 D1B 6 GLN A 25 SER A 31 -1 SHEET 5 D1B 6 ILE A 34 GLN A 40 -1 SHEET 6 D1B 6 PHE A 43 GLY A 47 -1 SHEET 1 D2A 3 LYS A 142 LEU A 149 0 SHEET 2 D2A 3 GLY A 111 GLU A 119 -1 SHEET 3 D2A 3 GLY A 99 ASN A 103 -1 SHEET 1 D2B 4 LYS A 166 ILE A 174 0 SHEET 2 D2B 4 GLY A 155 GLN A 163 -1 SHEET 3 D2B 4 SER A 127 SER A 132 -1 SHEET 4 D2B 4 LYS A 136 GLY A 140 -1 SSBOND 1 CYS A 16 CYS A 84 1555 1555 2.03 SSBOND 2 CYS A 130 CYS A 159 1555 1555 2.06 CRYST1 133.550 32.270 46.070 90.00 96.12 90.00 C 1 2 1 4 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 0.007488 0.000000 0.000803 0.00000 SCALE2 0.000000 0.030989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021831 0.00000