1BBF - Header Asymmetric Unit

HEADER GLYCOPROTEIN 29-APR-92 1BBF

TITLE ENERGY PARAMETERS IN POLYPEPTIDES. 10. IMPROVED GEOMETRICAL TITLE 2 PARAMETERS AND NONBONDED INTERACTIONS FOR USE IN THE TITLE 3 ECEPP(SLASH)3 ALGORITHM, WITH APPLICATION TO PROLINE- TITLE 4 CONTAINING PEPTIDES

COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE:; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE:; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 MOL_ID: 2; SOURCE 3 MOL_ID: 3

KEYWDS GLYCOPROTEIN

EXPDTA THEORETICAL MODEL

AUTHOR G.NEMETHY,K.D.GIBSON,K.A.PALMER,C.N.YOON,G.PATERLINI, AUTHOR 2 A.ZAGARI,S.RUMSEY,H.A.SCHERAGA

REVDAT 2 15-JAN-95 1BBF 1 HELIX REVDAT 1 31-JAN-94 1BBF 0

JRNL AUTH G.NEMETHY,K.D.GIBSON,K.A.PALMER,C.N.YOON, JRNL AUTH 2 G.PATERLINI,A.ZAGARI,S.RUMSEY,H.A.SCHERAGA JRNL TITL ENERGY PARAMETERS IN POLYPEPTIDES. 10. IMPROVED JRNL TITL 2 GEOMETRICAL PARAMETERS AND NONBONDED INTERACTIONS JRNL TITL 3 FOR USE IN THE ECEPP(SLASH)3 ALGORITHM, WITH JRNL TITL 4 APPLICATION TO PROLINE-CONTAINING PEPTIDES JRNL REF J.PHYS.CHEM. V. 96 6472 1992 JRNL REFN ASTM JPCHAX US ISSN 0022-3654

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.NEMETHY,H.A.SCHERAGA REMARK 1 TITL COMPUTATIONAL STUDIES OF THE STRUCTURE AND REMARK 1 TITL 2 ASSEMBLY OF TRIPLE-STRANDED MODELS OF COLLAGEN REMARK 1 REF BULL.INST.CHEM.RES.,KYOTO V. 66 398 1989 REMARK 1 REF 2 UNIV. REMARK 1 REFN ASTM BICRAS JA ISSN 0023-6071 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.H.MILLER,G.NEMETHY,H.A.SCHERAGA REMARK 1 TITL CALCULATION OF THE STRUCTURES OF COLLAGEN MODELS. REMARK 1 TITL 2 ROLE OF INTERCHAIN INTERACTIONS IN DETERMINING THE REMARK 1 TITL 3 TRIPLE-HELICAL COILED-COIL CONFORMATION. 2. REMARK 1 TITL 4 POLY(GLYCYL-PROLYL-HYDROXYPROLYL) REMARK 1 REF MACROMOLECULES V. 13 470 1980 REMARK 1 REFN ASTM MAMOBX US ISSN 0024-9297 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.H.MILLER,H.A.SCHERAGA REMARK 1 TITL CALCULATION OF THE STRUCTURES OF COLLAGEN MODELS. REMARK 1 TITL 2 ROLE OF INTERCHAIN INTERACTIONS IN DETERMINING THE REMARK 1 TITL 3 TRIPLE-HELICAL COILED-COIL CONFORMATION. I. REMARK 1 TITL 4 POLY(GLYCYL-PROLYL-PROLYL) REMARK 1 REF J.POLYM.SCI.,POLYM.SYMP. V. 54 171 1976 REMARK 1 REFN ASTM JPYCAQ US ISSN 0360-8905

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1BBF COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 5 REMARK 5 THE ENERGY OF THE STRUCTURE HAS BEEN MINIMIZED WITHOUT ANY REMARK 5 CONSTRAINTS. THIS TRIPLE HELIX IS DESCRIBED AS "STRUCTURE REMARK 5 TS" IN THE JOURNAL REFERENCE.

REMARK 6 REMARK 6 THIS STRUCTURE SERVES AS A COMPUTED REFERENCE MODEL REMARK 6 STRUCTURE OF A CONFORMATIONALLY RELAXED COLLAGEN-LIKE REMARK 6 POLY(TRIPEPTIDE) TRIPLE HELIX (REFERENCE 3). THE REMARK 6 COORDINATES OF A RELATED STRUCTURE, COMPUTED WITH THE REMARK 6 SYMMETRY CONSTRAINT OF STRUCTURAL EQUIVALENCE OF THE THREE REMARK 6 STRANDS, ARE CONTAINED IN PROTEIN DATA BANK ENTRY 1BBE.

REMARK 7 REMARK 7 THE COMPUTED MOLECULE CONSISTS OF THREE STRANDS WITH THE REMARK 7 FOLLOWING SEQUENCES FOR STRANDS 1, 2, AND 3, RESPECTIVELY: REMARK 7 N-ACETYL-(PRO-PRO-GLY)4-N'-METHYLAMIDE, REMARK 7 N-ACETYL-(GLY-PRO-PRO)4-N'-METHYLAMIDE, REMARK 7 N-ACETYL-(PRO-GLY-PRO)4-N'-METHYLAMIDE. THE THREE REMARK 7 POLYPEPTIDE CHAINS ARE POSITIONED IN A LEFT-HANDED REMARK 7 (COUNTERCLOCKWISE) SCREW-SYMMETRICAL ARRANGEMENT WITH REMARK 7 RESPECT TO A COMMON HELICAL AXIS (AS DEFINED IN REFERENCES REMARK 7 1,2). IN THIS ARRANGEMENT, EQUIVALENT RESIDUES (E.G. GLY) REMARK 7 ARE LONGITUDINALLY STAGGERED ALONG THE TRIPLE-HELICAL AXIS, REMARK 7 BY ONE AXIALLY PROJECTED RESIDUE-LENGTH (2.88 ANGSTROMS) REMARK 7 RELATIVE TO EACH OTHER. HOWEVER, BECAUSE OF THE CHOICE OF REMARK 7 THE SEQUENCES USED, THE N- AND C-TERMINI OF THE THREE REMARK 7 STRANDS ARE NON-STAGGERED, I.E. THE STRUCTURE REPRESENTS A REMARK 7 "BLUNT-END" FRAGMENT OF A COLLAGEN-LIKE TRIPLE HELIX.

REMARK 8 REMARK 8 THE COORDINATES ARE GIVEN IN A RIGHT-HANDED CARTESIAN REMARK 8 COORDINATE SYSTEM, DEFINED ACCORDING TO THE CONVENTION REMARK 8 USED IN ECEPP, I.E. IN TERMS OF THE POSITION OF ATOMS IN REMARK 8 THE FIRST FULL RESIDUE OF STRAND 1, AS FOLLOWS: THE N REMARK 8 ATOM IS AT THE ORIGIN, THE CA ATOM IS LOCATED ON THE REMARK 8 X-AXIS, AND THE Y-AXIS IS ORIENTED SO THAT THE AMIDE H REMARK 8 ATOM LIES IN THE XY-PLANE WITH A POSITIVE Y-COORDINATE.

REMARK 9 REMARK 9 HYDROGEN ATOMS IN THIS ENTRY HAVE BEEN ASSIGNED NAMES REMARK 9 CONSISTENT WITH THE RECOMMENDATIONS OF THE IUPAC-IUB REMARK 9 COMMISSION ON BIOCHEMICAL NOMENCLATURE (SEE E.G. REMARK 9 BIOCHEMISTRY 9, 3471-3479, (1970)).

REMARK 10 REMARK 10 CORRECTION. CORRECT RESIDUE ON HELIX RECORDS. 15-JAN-95.

REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL

REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.

REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 NME A 14 REMARK 465 NME B 14 REMARK 465 NME C 14

REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 C PRO B 13 N NME B 14 1.32 REMARK 500 C GLY A 13 N NME A 14 1.33 REMARK 500 C PRO C 13 N NME C 14 1.33

DBREF 1BBF A 2 13 UNP P22576 COLL_HSVSC 58 69 DBREF 1BBF B 2 13 UNP P22576 COLL_HSVSC 57 68 DBREF 1BBF C 2 13 UNP P22576 COLL_HSVSC 56 67

SEQRES 1 A 14 ACE PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY SEQRES 2 A 14 NME SEQRES 1 B 14 ACE GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 2 B 14 NME SEQRES 1 C 14 ACE PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO SEQRES 2 C 14 NME

MODRES 1BBF NME A 14 METHYLAMINE MODRES 1BBF NME B 14 METHYLAMINE MODRES 1BBF NME C 14 METHYLAMINE

HET ACE A 1 6 HET ACE B 1 6 HET ACE C 1 6 HET NME A 14 6 HET NME B 14 6 HET NME C 14 6

HETNAM ACE ACETYL GROUP HETNAM NME METHYLAMINE

FORMUL 1 ACE 3(C2 H4 O) FORMUL 4 NME 3(C H5 N)

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