3. Looking at 3D Structures
Let's look in detail at a PDB file: 1TSI, a complex of the enzyme triosephosphate isomerase with the inhibitor N-HYDROXY-4-PHOSPHONO-BUTANAMIDE.
HEADER ISOMERASE(INTRAMOLECULAR OXIDOREDUCTSE) 19-NOV-92 1TSI 1TSI 2 COMPND TRIOSEPHOSPHATE ISOMERASE (E.C.5.3.1.1) COMPLEX WITH 1TSIA 1 COMPND 2 N-HYDROXY-4-PHOSPHONO-BUTANAMIDE 1TSI 4 SOURCE (TRYPANOSOMA BRUCEI BRUCEI) 1TSI 5 AUTHOR C.L.M.J.VERLINDE 1TSI 6 REVDAT 2 15-OCT-94 1TSIA 1 COMPND 1TSIA 2 REVDAT 1 31-JAN-94 1TSI 0 1TSI 7 JRNL AUTH C.L.M.J.VERLINDE,C.J.WITMANS,T.PIJNING,K.H.KALK, 1TSI 8 JRNL AUTH 2 W.G.J.HOL 1TSI 9 JRNL TITL STRUCTURE OF THE COMPLEX BETWEEN TRYPANOSOMAL 1TSI 10 JRNL TITL 2 TRIOSEPHOSPHATE ISOMERASE AND 1TSI 11 JRNL TITL 3 N-HYDROXY-4-PHOSPHONO-BUTANAMIDE: BINDING AT THE 1TSI 12 JRNL TITL 4 ACTIVE SITE DESPITE AN "OPEN" FLEXIBLE LOOP 1TSI 13 JRNL REF PROTEIN SCI. V. 1 1578 1992 1TSI 14 JRNL REFN ASTM US ISSN 0961-8368 795 1TSI 15 REMARK 1 REFERENCE 1 1TSI 16 . . more references . REMARK 2 1TSI 39 REMARK 2 RESOLUTION. 2.84 ANGSTROMS 1TSI 40 REMARK 3 1TSI 41 REMARK 3 REFINEMENT. 1TSI 42 REMARK 3 PROGRAM TNT 1TSI 43 REMARK 3 AUTHORS TRONRUD,TEN EYCK,MATTHEWS 1TSI 44 REMARK 3 R VALUE 0.115 1TSI 45 REMARK 3 RMSD BOND DISTANCES 0.012 ANGSTROMS 1TSI 46 REMARK 3 RMSD BOND ANGLES 3.2 DEGREES 1TSI 47 REMARK 3 1TSI 48 REMARK 3 NUMBER OF REFLECTIONS 6530 1TSI 49 REMARK 3 RESOLUTION RANGE 6.0 - 2.84 ANGSTROMS 1TSI 50 REMARK 3 DATA CUTOFF 0.0 SIGMA(F) 1TSI 51 REMARK 3 PERCENT COMPLETION 0.958 1TSI 52 REMARK 3 1TSI 53 REMARK 3 NUMBER OF PROTEIN ATOMS 3771 1TSI 54 REMARK 3 NUMBER OF SOLVENT ATOMS 53 1TSI 55 REMARK 4 1TSI 56 REMARK 4 THE MODEL DOES NOT CONTAIN THE ATOMS CG,CD,OE1,NE2 OF 1TSI 57 REMARK 4 GLN 19, AND CD,OE1,OE2 OF GLU 323 DUE TO THE ABSENCE OF 1TSI 58 REMARK 4 INTERPRETABLE DENSITY. 1TSI 59 REMARK 5 1TSI 60 REMARK 5 THIS COORDINATE SET HAS BEEN DESIGNATED GTIM_4PBH_13MAY92 1TSI 61 REMARK 5 BY THE DEPOSITOR. 1TSI 62 REMARK 6 1TSI 63 REMARK 6 THE ASYMMETRIC UNIT CONSISTS OF A DIMER. THE TWO 1TSI 64 REMARK 6 MOLECULES HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*. 1TSI 65 REMARK 6 THE CRYSTALS USED FOR THIS STRUCTURE DETERMINATION WERE 1TSI 66 REMARK 6 GROWN IN THE PRESENCE OF 2.4M AMMONIUM SULFATE (SEE PROTEIN 1TSI 67 REMARK 6 DATA BANK ENTRY 2TIM), BUT BEFORE DATA COLLECTION THESE 1TSI 68 REMARK 6 CRYSTALS WERE TRANSFERRED TO A MOTHER LIQUOR WITHOUT 1TSI 69 REMARK 6 SULFATE. THE ACTIVE SITE OF SUBUNIT *A* CONTAINS THE 1TSI 70 REMARK 6 INHIBITOR N-HYDROXY-4-PHOSPHONO-BUTANAMIDE 1TSI 71 REMARK 6 (KI = 0.3 * 10**-3 M). IN THIS ENTRY THE FLEXIBLE LOOP 1TSI 72 REMARK 6 (LOOP 6) OF EACH SUBUNIT IS IN AN OPEN CONFORMATION. 1TSI 73 REMARK 7 1TSI 74 REMARK 7 SECONDARY STRUCTURE SPECIFICATIONS WERE MADE BY USE OF 1TSI 75 REMARK 7 PROGRAM *DSSP* OF W. KABSCH AND C. SANDER. 1TSI 76 REMARK 8 1TSI 77 REMARK 8 THE SHEETS PRESENTED AS *A* AND *B* ON SHEET RECORDS BELOW 1TSI 78 REMARK 8 ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THESE ARE 1TSI 79 REMARK 8 REPRESENTED BY NINE-STRANDED SHEETS IN WHICH THE FIRST AND 1TSI 80 REMARK 8 LAST STRANDS ARE IDENTICAL. 1TSI 81 SEQRES 1 A 250 MET SER LYS PRO GLN PRO ILE ALA ALA ALA ASN TRP LYS 1TSI 82 . . more sequence records . HET 4PB 600 11 N-HYDROXY-4-PHOSPHONO-BUTANAMIDE 1TSI 122 FORMUL 3 4PB C4 H8 N1 O5 P1 -- 1TSI 123 FORMUL 4 HOH *53(H2 O1) 1TSI 124 HELIX 1 1A GLN A 18 SER A 30 1 1TSI 125 . . more helix description . SHEET 1 A 9 ILE A 7 ASN A 11 0 1TSI 147 . . more sheet description . CRYST1 113.340 97.150 46.450 90.00 90.00 90.00 P 21 21 21 8 1TSI 165 ORIGX1 1.000000 0.000000 0.000000 0.00000 1TSI 166 ORIGX2 0.000000 1.000000 0.000000 0.00000 1TSI 167 ORIGX3 0.000000 0.000000 1.000000 0.00000 1TSI 168 SCALE1 0.008823 0.000000 0.000000 0.00000 1TSI 169 SCALE2 0.000000 0.010293 0.000000 0.00000 1TSI 170 SCALE3 0.000000 0.000000 0.021529 0.00000 1TSI 171 ATOM 1 N SER A 2 28.425 57.398 19.636 1.00 32.17 1TSI 172 . . more ATOM records . ATOM 3772 OXT GLN B 250 40.144 -2.108 -21.613 1.00 69.66 1TSI3943 TER 3773 GLN B 250 1TSI3944 HETATM 3774 C1 4PB 600 34.802 29.953 22.871 1.00 27.54 1TSI3945 . . more HETATM records . CONECT 3774 3775 3781 1TSI4009 CONECT 3775 3774 3776 1TSI4010 CONECT 3776 3775 3777 1TSI4011 CONECT 3777 3776 3778 3779 1TSI4012 CONECT 3778 3777 3780 1TSI4013 CONECT 3779 3777 1TSI4014 CONECT 3780 3778 1TSI4015 CONECT 3781 3774 3782 3783 3784 1TSI4016 CONECT 3782 3781 1TSI4017 CONECT 3783 3781 1TSI4018 CONECT 3784 3781 1TSI4019 MASTER 69 0 1 22 18 0 0 6 3835 2 11 40 1TSIA 6 END 1TSI4021
Here is some info about the records: