10 20 30 40 50 60 70 80 1JL4 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER IMMUNE SYSTEM 15-JUL-01 1JL4
TITLE CRYSTAL STRUCTURE OF THE HUMAN CD4 N-TERMINAL TWO DOMAIN TITLE 2 FRAGMENT COMPLEXED TO A CLASS II MHC MOLECULE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K COMPND 3 ALPHA CHAIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K COMPND 8 BETA CHAIN; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: OVOTRANSFERRIN; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: CONALBUMIN; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD4; COMPND 18 CHAIN: D; COMPND 19 SYNONYM: T-CELL SURFACE ANTIGEN T4/LEU-3; COMPND 20 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 13 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 17 ORGANISM_COMMON: CHICKEN; SOURCE 18 ORGANISM_TAXID: 9031; SOURCE 19 EXPRESSION_SYSTEM: GALLUS GALLUS; SOURCE 20 EXPRESSION_SYSTEM_COMMON: CHICKEN; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 9031; SOURCE 22 MOL_ID: 4; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606; SOURCE 26 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 27 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 10029
KEYWDS PROTEIN-PROTEIN COMPLEX, IMMUNE SYSTEM
EXPDTA X-RAY DIFFRACTION
AUTHOR J.-H.WANG,R.MEIJERS,E.L.REINHERZ
REVDAT 3 24-FEB-09 1JL4 1 VERSN REVDAT 2 01-APR-03 1JL4 1 JRNL REVDAT 1 19-SEP-01 1JL4 0
JRNL AUTH J.H.WANG,R.MEIJERS,Y.XIONG,J.H.LIU,T.SAKIHAMA, JRNL AUTH 2 R.ZHANG,A.JOACHIMIAK,E.L.REINHERZ JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN CD4 N-TERMINAL JRNL TITL 2 TWO-DOMAIN FRAGMENT COMPLEXED TO A CLASS II MHC JRNL TITL 3 MOLECULE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 98 10799 2001 JRNL REFN ISSN 0027-8424 JRNL PMID 11535811 JRNL DOI 10.1073/PNAS.191124098
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 4.30 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.0 REMARK 3 NUMBER OF REFLECTIONS : 6432 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.428 REMARK 3 R VALUE (WORKING SET) : 0.420 REMARK 3 FREE R VALUE : 0.453 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 649 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4474 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS MODEL IS BASED ON HIGH REMARK 3 RESOLUTION STRUCTURES OF THE INDIVIDUAL COMPONENTS AND ONLY REMARK 3 RIGID BODY REFINEMENT OF THE INDIVIDUAL DOMAINS WAS APPLIED. REMARK 3 THE RIGID BODIES CONSISTED OF RESIDUE RANGES A 5 TO A 85, A 86 REMARK 3 TO A 181, B 5 TO B 85, B 86 TO B 190, C 131 TO C 146, D 1 TO D REMARK 3 97 AND D 98 TO D 178
REMARK 4 REMARK 4 1JL4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-01. REMARK 100 THE RCSB ID CODE IS RCSB013897.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7428 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.15200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE, EPMR, FFFEAR REMARK 200 STARTING MODEL: 1IAK AND 3CD4 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG 4,000/0.2M LI2SO4/0.1M REMARK 280 TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 51.92300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.88450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.96150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.92300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 25.96150 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 77.88450 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS D 1 N CA CB REMARK 470 TRP D 28 CH2 REMARK 470 ARG D 54 NH1 NH2 REMARK 470 ARG D 58 NH1 NH2 REMARK 470 ARG D 59 NH1 NH2 REMARK 470 TRP D 62 CH2 REMARK 470 TYR D 82 OH REMARK 470 ASP D 105 CG OD1 OD2 REMARK 470 ARG D 131 NH1 NH2 REMARK 470 ARG D 134 NH1 NH2 REMARK 470 TRP D 157 CH2
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 CE MET B 160 OE1 GLN D 40 1.41 REMARK 500 O PRO B 56 CD1 ILE C 143 1.47 REMARK 500 SD MET B 160 NE2 GLN D 40 1.57 REMARK 500 CG ARG A 53 O ASN C 132 1.73 REMARK 500 CE MET B 160 CD GLN D 40 1.82 REMARK 500 OG1 THR B 85 CE1 HIS C 134 2.00 REMARK 500 O ARG A 53 N HIS C 134 2.01 REMARK 500 NE2 GLN A 88 CB SER D 60 2.03 REMARK 500 CE MET B 160 NE2 GLN D 40 2.04 REMARK 500 O LEU A 51 ND2 ASN C 132 2.09 REMARK 500 NZ LYS A 94 OD2 ASP B 152 2.11 REMARK 500 O ARG A 53 CB HIS C 134 2.14 REMARK 500 NE ARG A 52 NE2 HIS C 134 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CD2 HIS D 107 CB LEU D 177 8665 0.41 REMARK 500 CD GLN A 57 CD GLN A 57 5555 0.51 REMARK 500 CG GLN A 57 NE2 GLN A 57 5555 0.91 REMARK 500 NE2 GLN B 64 CG GLU C 144 5555 0.97 REMARK 500 CG HIS D 107 CB LEU D 177 8665 1.10 REMARK 500 CG HIS D 107 CA LEU D 177 8665 1.14 REMARK 500 NH1 ARG B 130 NH2 ARG B 130 5556 1.18 REMARK 500 NE2 HIS D 107 CB LEU D 177 8665 1.24 REMARK 500 CG GLN A 57 CD GLN A 57 5555 1.28 REMARK 500 CD GLN A 57 NE2 GLN A 57 5555 1.29 REMARK 500 C HIS D 107 CD2 LEU D 177 8665 1.29 REMARK 500 CD GLN B 64 CG GLU C 144 5555 1.31 REMARK 500 O HIS D 107 CD2 LEU D 177 8665 1.39 REMARK 500 N GLY B 135 O THR B 181 5556 1.50 REMARK 500 CZ ARG B 130 NH1 ARG B 130 5556 1.54 REMARK 500 CD2 HIS D 107 CG LEU D 177 8665 1.56 REMARK 500 CD2 HIS D 107 CA LEU D 177 8665 1.57 REMARK 500 OE1 GLN B 64 CG GLU C 144 5555 1.63 REMARK 500 CG GLN A 57 OE1 GLN A 57 5555 1.67 REMARK 500 CB THR D 106 CB SER D 154 8665 1.68 REMARK 500 CG2 THR B 51 OG SER D 127 8665 1.69 REMARK 500 NH2 ARG B 34 OE1 GLN D 165 8665 1.71 REMARK 500 CD GLN A 57 OE1 GLN A 57 5555 1.72 REMARK 500 CA GLN B 64 OE2 GLU C 144 5555 1.74 REMARK 500 CB HIS D 107 O VAL D 176 8665 1.75 REMARK 500 OE1 GLN B 64 CD GLU C 144 5555 1.77 REMARK 500 CD GLN B 64 CD GLU C 144 5555 1.77 REMARK 500 NZ LYS B 128 OE1 GLU B 137 5556 1.80 REMARK 500 CZ ARG B 130 NH2 ARG B 130 5556 1.80 REMARK 500 N HIS D 107 CG1 VAL D 175 8665 1.82 REMARK 500 ND1 HIS D 107 CB LEU D 177 8665 1.83 REMARK 500 CZ ARG B 130 CZ ARG B 130 5556 1.83 REMARK 500 NH1 ARG B 130 NH1 ARG B 130 5556 1.83 REMARK 500 OE1 GLN A 57 NE2 GLN A 57 5555 1.86 REMARK 500 CE1 HIS D 107 CB LEU D 177 8665 1.86 REMARK 500 CD GLN B 64 OE2 GLU C 144 5555 1.86 REMARK 500 CD2 LEU A 99 OD1 ASP A 130 6565 1.88 REMARK 500 CB HIS D 107 CA LEU D 177 8665 1.89 REMARK 500 CG HIS D 107 CG LEU D 177 8665 1.91 REMARK 500 C ASN B 134 O THR B 181 5556 1.91 REMARK 500 NE2 GLN B 64 CB GLU C 144 5555 1.91 REMARK 500 OG1 THR D 106 CB SER D 154 8665 1.92 REMARK 500 NE2 GLN B 64 CD GLU C 144 5555 1.93 REMARK 500 CA GLY B 135 O THR B 181 5556 1.99 REMARK 500 ND1 HIS D 107 CA LEU D 177 8665 2.02 REMARK 500 N LEU D 108 CD2 LEU D 177 8665 2.05 REMARK 500 OE1 GLN A 61 NE2 GLN A 61 5555 2.06 REMARK 500 NH2 ARG B 34 CD GLN D 165 8665 2.08 REMARK 500 C HIS D 107 CG LEU D 177 8665 2.08 REMARK 500 OE1 GLN B 64 OE2 GLU C 144 5555 2.12 REMARK 500 REMARK 500 THIS ENTRY HAS 55 CLOSE CONTACTS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 THR A 80 C PRO A 81 N 0.122 REMARK 500 ALA A 89 C THR A 90 N 0.231 REMARK 500 GLU B 84 C LYS B 84A N -0.153 REMARK 500 THR B 89 C SER B 90 N -0.220 REMARK 500 GLY D 99 C LEU D 100 N 0.326 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 ARG B 70 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG B 70 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 THR B 89 O - C - N ANGL. DEV. = -13.8 DEGREES REMARK 500 TRP D 28 CD1 - CG - CD2 ANGL. DEV. = 7.9 DEGREES REMARK 500 TRP D 28 CE2 - CD2 - CG ANGL. DEV. = -6.7 DEGREES REMARK 500 TRP D 62 CD1 - CG - CD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 TRP D 62 CB - CG - CD1 ANGL. DEV. = -8.3 DEGREES REMARK 500 TRP D 62 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 TRP D 62 CG - CD2 - CE3 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP D 157 CD1 - CG - CD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 TRP D 157 CE2 - CD2 - CG ANGL. DEV. = -5.6 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 39 60.02 61.26 REMARK 500 ASN A 78 53.21 70.96 REMARK 500 PHE A 113 123.49 -173.64 REMARK 500 PRO A 115 56.71 -68.82 REMARK 500 SER A 125 16.83 59.11 REMARK 500 PRO A 180 -179.94 -63.27 REMARK 500 ASN B 33 -96.50 60.01 REMARK 500 THR B 89 -85.68 -130.82 REMARK 500 ALA B 108 104.49 -170.97 REMARK 500 THR B 139 -67.84 -130.16 REMARK 500 TRP B 153 31.79 75.35 REMARK 500 SER C 145 -156.36 44.16 REMARK 500 LYS D 8 131.29 -39.63 REMARK 500 ALA D 18 -164.96 -124.48 REMARK 500 SER D 19 -156.68 -103.81 REMARK 500 GLN D 20 73.43 36.39 REMARK 500 LYS D 21 95.50 -43.64 REMARK 500 LYS D 22 141.17 -178.16 REMARK 500 SER D 23 77.29 -61.85 REMARK 500 ILE D 24 -145.46 -96.07 REMARK 500 ASP D 56 -176.86 177.81 REMARK 500 ASP D 80 166.62 179.76 REMARK 500 GLU D 87 -121.27 47.10 REMARK 500 ASP D 88 45.97 -104.69 REMARK 500 ASN D 103 6.87 -63.85 REMARK 500 ASP D 105 -109.80 32.62 REMARK 500 HIS D 107 89.66 55.46 REMARK 500 PRO D 122 -31.30 -34.81 REMARK 500 SER D 124 126.51 118.68 REMARK 500 PRO D 126 -167.21 -118.93 REMARK 500 ARG D 134 52.23 -142.75 REMARK 500 LYS D 136 130.57 -25.08 REMARK 500 SER D 147 -53.99 -27.45 REMARK 500 LEU D 151 -27.25 -37.13 REMARK 500 ASN D 164 -170.10 61.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE D 43 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY D 99 16.96 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IAK RELATED DB: PDB REMARK 900 MURINE CLASS II MHC MOLECULE REMARK 900 RELATED ID: 3CD4 RELATED DB: PDB REMARK 900 HUMAN CD4 FRAGMENT (DOMAIN I AND II) REMARK 900 RELATED ID: 1WIO RELATED DB: PDB REMARK 900 HUMAN CD4 FRAGMENT (DOMAIN I TO IV) REMARK 900 RELATED ID: 1G9M RELATED DB: PDB REMARK 900 HIV GP120 GLYCOPROTEIN COMPLEXED WITH HUMAN CD4 FRAGMENT REMARK 900 (DOMAIN I AND II)
DBREF 1JL4 A 5 181 UNP P01910 HA2K_MOUSE 31 208 DBREF 1JL4 B 7 190 UNP P06343 HB2K_MOUSE 34 216 DBREF 1JL4 C 134 146 UNP P02789 TRFE_CHICK 153 165 DBREF 1JL4 D 1 178 UNP P01730 CD4_HUMAN 26 203
SEQADV 1JL4 GLY B 5 UNP P06343 CLONING ARTIFACT SEQADV 1JL4 SER B 6 UNP P06343 CLONING ARTIFACT SEQADV 1JL4 THR B 181 UNP P06343 LYS 207 CONFLICT SEQADV 1JL4 GLY C 131 UNP P02789 CLONING ARTIFACT SEQADV 1JL4 ASN C 132 UNP P02789 CLONING ARTIFACT SEQADV 1JL4 SER C 133 UNP P02789 CLONING ARTIFACT
SEQRES 1 A 178 HIS VAL GLY SER TYR GLY ILE THR VAL TYR GLN SER PRO SEQRES 2 A 178 GLY ASP ILE GLY GLN TYR THR PHE GLU PHE ASP GLY ASP SEQRES 3 A 178 GLU LEU PHE TYR VAL ASP LEU ASP LYS LYS GLU THR VAL SEQRES 4 A 178 TRP MET LEU PRO GLU PHE ALA GLN LEU ARG ARG PHE GLU SEQRES 5 A 178 PRO GLN GLY GLY LEU GLN ASN ILE ALA THR GLY LYS HIS SEQRES 6 A 178 ASN LEU GLU ILE LEU THR LYS ARG SER ASN SER THR PRO SEQRES 7 A 178 ALA THR ASN GLU ALA PRO GLN ALA THR VAL PHE PRO LYS SEQRES 8 A 178 SER PRO VAL LEU LEU GLY GLN PRO ASN THR LEU ILE CYS SEQRES 9 A 178 PHE VAL ASP ASN ILE PHE PRO PRO VAL ILE ASN ILE THR SEQRES 10 A 178 TRP LEU ARG ASN SER LYS SER VAL THR ASP GLY VAL TYR SEQRES 11 A 178 GLU THR SER PHE PHE VAL ASN ARG ASP TYR SER PHE HIS SEQRES 12 A 178 LYS LEU SER TYR LEU THR PHE ILE PRO SER ASP ASP ASP SEQRES 13 A 178 ILE TYR ASP CYS LYS VAL GLU HIS TRP GLY LEU GLU GLU SEQRES 14 A 178 PRO VAL LEU LYS HIS TRP GLU PRO GLU SEQRES 1 B 185 GLY SER PHE VAL HIS GLN PHE GLN PRO PHE CYS TYR PHE SEQRES 2 B 185 THR ASN GLY THR GLN ARG ILE ARG LEU VAL ILE ARG TYR SEQRES 3 B 185 ILE TYR ASN ARG GLU GLU TYR VAL ARG PHE ASP SER ASP SEQRES 4 B 185 VAL GLY GLU TYR ARG ALA VAL THR GLU LEU GLY ARG PRO SEQRES 5 B 185 ASP ALA GLU TYR TRP ASN LYS GLN TYR LEU GLU ARG THR SEQRES 6 B 185 ARG ALA GLU LEU ASP THR VAL CYS ARG HIS ASN TYR GLU SEQRES 7 B 185 LYS THR GLU THR PRO THR SER LEU ARG ARG LEU GLU GLN SEQRES 8 B 185 PRO SER VAL VAL ILE SER LEU SER ARG THR GLU ALA LEU SEQRES 9 B 185 ASN HIS HIS ASN THR LEU VAL CYS SER VAL THR ASP PHE SEQRES 10 B 185 TYR PRO ALA LYS ILE LYS VAL ARG TRP PHE ARG ASN GLY SEQRES 11 B 185 GLN GLU GLU THR VAL GLY VAL SER SER THR GLN LEU ILE SEQRES 12 B 185 ARG ASN GLY ASP TRP THR PHE GLN VAL LEU VAL MET LEU SEQRES 13 B 185 GLU MET THR PRO ARG ARG GLY GLU VAL TYR THR CYS HIS SEQRES 14 B 185 VAL GLU HIS PRO SER LEU THR SER PRO ILE THR VAL GLU SEQRES 15 B 185 TRP ARG ALA SEQRES 1 C 16 GLY ASN SER HIS ARG GLY ALA ILE GLU TRP GLU GLY ILE SEQRES 2 C 16 GLU SER GLY SEQRES 1 D 178 LYS LYS VAL VAL LEU GLY LYS LYS GLY ASP THR VAL GLU SEQRES 2 D 178 LEU THR CYS THR ALA SER GLN LYS LYS SER ILE GLN PHE SEQRES 3 D 178 HIS TRP LYS ASN SER ASN GLN ILE LYS ILE LEU GLY ASN SEQRES 4 D 178 GLN GLY SER PHE LEU THR LYS GLY PRO SER LYS LEU ASN SEQRES 5 D 178 ASP ARG ALA ASP SER ARG ARG SER LEU TRP ASP GLN GLY SEQRES 6 D 178 ASN PHE PRO LEU ILE ILE LYS ASN LEU LYS ILE GLU ASP SEQRES 7 D 178 SER ASP THR TYR ILE CYS GLU VAL GLU ASP GLN LYS GLU SEQRES 8 D 178 GLU VAL GLN LEU LEU VAL PHE GLY LEU THR ALA ASN SER SEQRES 9 D 178 ASP THR HIS LEU LEU GLN GLY GLN SER LEU THR LEU THR SEQRES 10 D 178 LEU GLU SER PRO PRO GLY SER SER PRO SER VAL GLN CYS SEQRES 11 D 178 ARG SER PRO ARG GLY LYS ASN ILE GLN GLY GLY LYS THR SEQRES 12 D 178 LEU SER VAL SER GLN LEU GLU LEU GLN ASP SER GLY THR SEQRES 13 D 178 TRP THR CYS THR VAL LEU GLN ASN GLN LYS LYS VAL GLU SEQRES 14 D 178 PHE LYS ILE ASP ILE VAL VAL LEU ALA
HELIX 1 1 LEU A 45 LEU A 51 5 7 HELIX 2 2 GLU A 55 ASN A 78 1 24 HELIX 3 3 ASN B 19 GLN B 22 5 4 HELIX 4 4 THR B 51 LEU B 53 5 3 HELIX 5 5 GLY B 54 TYR B 67 1 12 HELIX 6 6 TYR B 67 ALA B 73 1 7 HELIX 7 7 ALA B 73 VAL B 78 1 6 HELIX 8 8 VAL B 78 THR B 85 1 9 HELIX 9 9 THR B 89 ARG B 93 5 5 HELIX 10 10 ARG D 58 GLY D 65 5 8 HELIX 11 11 LYS D 75 SER D 79 5 5 HELIX 12 12 GLU D 150 SER D 154 5 5
SHEET 1 A 8 GLU A 40 TRP A 43 0 SHEET 2 A 8 ASP A 29 ASP A 35 -1 O TYR A 33 N VAL A 42 SHEET 3 A 8 ILE A 19 PHE A 26 -1 O TYR A 22 N VAL A 34 SHEET 4 A 8 VAL A 6 SER A 15 -1 N SER A 8 O GLU A 25 SHEET 5 A 8 PHE B 7 THR B 18 -1 N PHE B 7 O SER A 15 SHEET 6 A 8 ARG B 23 TYR B 32 -1 O ARG B 23 N THR B 18 SHEET 7 A 8 GLU B 35 ASP B 41 -1 O GLU B 35 N TYR B 32 SHEET 8 A 8 TYR B 47 ALA B 49 -1 O ARG B 48 N ARG B 39 SHEET 1 B 2 ARG A 53 PHE A 54 0 SHEET 2 B 2 SER C 133 HIS C 134 1 N HIS C 134 O ARG A 53 SHEET 1 C 4 GLN A 88 PRO A 93 0 SHEET 2 C 4 ASN A 103 ILE A 112 -1 N ILE A 106 O PHE A 92 SHEET 3 C 4 PHE A 145 PHE A 153 -1 O PHE A 145 N ILE A 112 SHEET 4 C 4 VAL A 132 GLU A 134 -1 O TYR A 133 N TYR A 150 SHEET 1 D 4 GLN A 88 PRO A 93 0 SHEET 2 D 4 ASN A 103 ILE A 112 -1 N ILE A 106 O PHE A 92 SHEET 3 D 4 PHE A 145 PHE A 153 -1 O PHE A 145 N ILE A 112 SHEET 4 D 4 PHE A 138 VAL A 139 -1 N PHE A 138 O HIS A 146 SHEET 1 E 4 LYS A 126 SER A 127 0 SHEET 2 E 4 ASN A 118 ARG A 123 -1 N ARG A 123 O LYS A 126 SHEET 3 E 4 TYR A 161 GLU A 166 -1 O ASP A 162 N LEU A 122 SHEET 4 E 4 VAL A 174 TRP A 178 -1 N VAL A 174 O VAL A 165 SHEET 1 F 4 SER B 98 LEU B 103 0 SHEET 2 F 4 ASN B 113 PHE B 122 -1 N VAL B 116 O SER B 102 SHEET 3 F 4 PHE B 155 MET B 163 -1 N PHE B 155 O PHE B 122 SHEET 4 F 4 VAL B 142 SER B 144 -1 O SER B 143 N MET B 160 SHEET 1 G 4 SER B 98 LEU B 103 0 SHEET 2 G 4 ASN B 113 PHE B 122 -1 N VAL B 116 O SER B 102 SHEET 3 G 4 PHE B 155 MET B 163 -1 N PHE B 155 O PHE B 122 SHEET 4 G 4 ILE B 148 ARG B 149 -1 N ILE B 148 O GLN B 156 SHEET 1 H 4 GLN B 136 GLU B 138 0 SHEET 2 H 4 LYS B 128 ARG B 133 -1 O TRP B 131 N GLU B 138 SHEET 3 H 4 VAL B 170 GLU B 176 -1 N THR B 172 O PHE B 132 SHEET 4 H 4 ILE B 184 ARG B 189 -1 O ILE B 184 N VAL B 175 SHEET 1 I 6 PHE D 43 THR D 45 0 SHEET 2 I 6 LYS D 35 GLN D 40 -1 O GLY D 38 N THR D 45 SHEET 3 I 6 PHE D 26 ASN D 30 -1 O PHE D 26 N ASN D 39 SHEET 4 I 6 ASP D 80 VAL D 86 -1 O ILE D 83 N LYS D 29 SHEET 5 I 6 GLN D 89 ALA D 102 -1 N GLN D 89 O VAL D 86 SHEET 6 I 6 LYS D 2 LYS D 7 1 O LYS D 2 N GLN D 94 SHEET 1 J 7 PHE D 43 THR D 45 0 SHEET 2 J 7 LYS D 35 GLN D 40 -1 O GLY D 38 N THR D 45 SHEET 3 J 7 PHE D 26 ASN D 30 -1 O PHE D 26 N ASN D 39 SHEET 4 J 7 ASP D 80 VAL D 86 -1 O ILE D 83 N LYS D 29 SHEET 5 J 7 GLN D 89 ALA D 102 -1 N GLN D 89 O VAL D 86 SHEET 6 J 7 LEU D 114 GLU D 119 -1 N THR D 117 O THR D 101 SHEET 7 J 7 THR D 143 VAL D 146 -1 N LEU D 144 O LEU D 116 SHEET 1 K 3 VAL D 12 LEU D 14 0 SHEET 2 K 3 LEU D 69 ILE D 71 -1 O LEU D 69 N LEU D 14 SHEET 3 K 3 ALA D 55 ASP D 56 -1 O ASP D 56 N ILE D 70 SHEET 1 L 2 LEU D 108 LEU D 109 0 SHEET 2 L 2 VAL D 176 LEU D 177 1 N LEU D 177 O LEU D 108 SHEET 1 M 4 GLN D 139 GLY D 140 0 SHEET 2 M 4 SER D 127 GLN D 129 -1 O VAL D 128 N GLY D 140 SHEET 3 M 4 CYS D 159 GLN D 163 -1 O THR D 160 N GLN D 129 SHEET 4 M 4 LYS D 166 PHE D 170 -1 N LYS D 166 O GLN D 163 SHEET 1 N 2 GLY D 155 THR D 156 0 SHEET 2 N 2 ASP D 173 ILE D 174 -1 O ILE D 174 N GLY D 155
SSBOND 1 CYS A 107 CYS A 163 1555 1555 2.04 SSBOND 2 CYS B 15 CYS B 79 1555 1555 2.06 SSBOND 3 CYS B 117 CYS B 173 1555 1555 2.02 SSBOND 4 CYS D 16 CYS D 84 1555 1555 2.03 SSBOND 5 CYS D 130 CYS D 159 1555 1555 2.02
CISPEP 1 SER A 15 PRO A 16 0 0.29 CISPEP 2 PHE A 113 PRO A 114 0 -0.18 CISPEP 3 TYR B 123 PRO B 124 0 0.20
CRYST1 145.195 145.195 103.846 90.00 90.00 90.00 P 43 2 2 8
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 0.006887 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006887 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009630 0.00000