1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 CIS PROLINE - PRO 75 Clore, G.M. Qin, J. Gronenborn, A.M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK Structure STRUE6 2005 0969-2126 3 289 297 10.1016/S0969-2126(01)00159-9 7788295 Solution structure of human thioredoxin in a mixed disulfide intermediate complex with its target peptide from the transcription factor NF kappa B. 1995 10.2210/pdb1mdi/pdb pdb_00001mdi 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 11592.125 THIOREDOXIN 1 man polymer 1557.755 TARGET SITE IN HUMAN NFKB 1 man polymer 18.015 water 6 nat water no no MVKQIESKTAFQEALDAAGDKLVVVDFSATWCGPAKMIKPFFHSLSEKYSNVIFLEVDVDDAQDVASEAEVKATPTFQFF KKGQKVGEFSGANKEKLEATINELV MVKQIESKTAFQEALDAAGDKLVVVDFSATWCGPAKMIKPFFHSLSEKYSNVIFLEVDVDDAQDVASEAEVKATPTFQFF KKGQKVGEFSGANKEKLEATINELV A polypeptide(L) no no FRFRYVCEGPSHG FRFRYVCEGPSHG B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human Homo sample 9606 Homo sapiens database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1995-06-03 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _struct_ref_seq_dif.details Y BNL 1995-02-27 REL REL HOH water AT POSITION 74 THR WAS FOUND BY WOLMAN ET AL., JOURNAL OF BIOCHEMISTRY 263, 15506 (1988). 1 THE 3D STRUCTURE OF THE HUMAN THIOREDOXIN-NFKB PEPTIDE COMPLEX IN SOLUTION BY NMR IS BASED ON 3213 EXPERIMENTAL RESTRAINTS COMPRISING: 2546 STRUCTURE USEFUL INTERPROTON DISTANCE RESTRAINTS 36 RESTRAINTS FOR 18 BACKBONE H-BONDS 44 RESTRAINTS FOR 6 BOUND WATER MOLECULES 300 TORSION ANGLE RESTRAINTS (104 PHI, 76 PSI, 78 CHI1 AND 31 CHI2 FOR HUMAN THIOREDOXIN, AND 7 CHI1 AND 4 CHI2 RESTRAINTS FOR THE NFKB PEPTIDE) 88 HN-HALPHA THREE-BOND COUPLING CONSTANTS 102 13CALPHA AND 97 13CB CHEMICAL SHIFT RESTRAINTS. THE BREAKDOWN OF THE INTERPROTON DISTANCE RESTRAINTS IS AS FOLLOWS: INTRAMOLECULAR HTRX RESTRAINTS: 503 SEQUENTIAL 437 SHORT RANGE (1 < |I-J|<=5) 727 LONG RANGE (|I-J|>5) 690 INTRARESIDUE INTRAMOLECULAR PEPTIDE RESTRAINTS: 115 INTERMOLECULAR HTRX-NFKB: 74 THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & GRONENBORN, A.M. (1988) FEBS LETT 229, 317 - 324. ALL STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE. THE STRUCTURE FOUND IN PDB ENTRY 1MDI IS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 60 DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES 1 - 105 OF HTRX AND RESIDUES 57 - 67 OF THE PEPTIDE AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE LAST NUMBER COLUMN IN THIS SET OF COORDINATES (THE B-FACTOR COLUMN IN X-RAY STRUCTURES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE. THE NUMBERS IN THE LAST COLUMN OF THE INDIVIDUAL STRUCTURES HAVE NO MEANING. HOH 1 3 HOH HOH 106 A HOH 2 3 HOH HOH 107 A HOH 3 3 HOH HOH 108 A HOH 4 3 HOH HOH 109 A HOH 5 3 HOH HOH 110 A HOH 6 3 HOH HOH 111 A MET 1 n 1 MET 1 A VAL 2 n 2 VAL 2 A LYS 3 n 3 LYS 3 A GLN 4 n 4 GLN 4 A ILE 5 n 5 ILE 5 A GLU 6 n 6 GLU 6 A SER 7 n 7 SER 7 A LYS 8 n 8 LYS 8 A THR 9 n 9 THR 9 A ALA 10 n 10 ALA 10 A PHE 11 n 11 PHE 11 A GLN 12 n 12 GLN 12 A GLU 13 n 13 GLU 13 A ALA 14 n 14 ALA 14 A LEU 15 n 15 LEU 15 A ASP 16 n 16 ASP 16 A ALA 17 n 17 ALA 17 A ALA 18 n 18 ALA 18 A GLY 19 n 19 GLY 19 A ASP 20 n 20 ASP 20 A LYS 21 n 21 LYS 21 A LEU 22 n 22 LEU 22 A VAL 23 n 23 VAL 23 A VAL 24 n 24 VAL 24 A VAL 25 n 25 VAL 25 A ASP 26 n 26 ASP 26 A PHE 27 n 27 PHE 27 A SER 28 n 28 SER 28 A ALA 29 n 29 ALA 29 A THR 30 n 30 THR 30 A TRP 31 n 31 TRP 31 A CYS 32 n 32 CYS 32 A GLY 33 n 33 GLY 33 A PRO 34 n 34 PRO 34 A ALA 35 n 35 ALA 35 A LYS 36 n 36 LYS 36 A MET 37 n 37 MET 37 A ILE 38 n 38 ILE 38 A LYS 39 n 39 LYS 39 A PRO 40 n 40 PRO 40 A PHE 41 n 41 PHE 41 A PHE 42 n 42 PHE 42 A HIS 43 n 43 HIS 43 A SER 44 n 44 SER 44 A LEU 45 n 45 LEU 45 A SER 46 n 46 SER 46 A GLU 47 n 47 GLU 47 A LYS 48 n 48 LYS 48 A TYR 49 n 49 TYR 49 A SER 50 n 50 SER 50 A ASN 51 n 51 ASN 51 A VAL 52 n 52 VAL 52 A ILE 53 n 53 ILE 53 A PHE 54 n 54 PHE 54 A LEU 55 n 55 LEU 55 A GLU 56 n 56 GLU 56 A VAL 57 n 57 VAL 57 A ASP 58 n 58 ASP 58 A VAL 59 n 59 VAL 59 A ASP 60 n 60 ASP 60 A ASP 61 n 61 ASP 61 A ALA 62 n 62 ALA 62 A GLN 63 n 63 GLN 63 A ASP 64 n 64 ASP 64 A VAL 65 n 65 VAL 65 A ALA 66 n 66 ALA 66 A SER 67 n 67 SER 67 A GLU 68 n 68 GLU 68 A ALA 69 n 69 ALA 69 A GLU 70 n 70 GLU 70 A VAL 71 n 71 VAL 71 A LYS 72 n 72 LYS 72 A ALA 73 n 73 ALA 73 A THR 74 n 74 THR 74 A PRO 75 n 75 PRO 75 A THR 76 n 76 THR 76 A PHE 77 n 77 PHE 77 A GLN 78 n 78 GLN 78 A PHE 79 n 79 PHE 79 A PHE 80 n 80 PHE 80 A LYS 81 n 81 LYS 81 A LYS 82 n 82 LYS 82 A GLY 83 n 83 GLY 83 A GLN 84 n 84 GLN 84 A LYS 85 n 85 LYS 85 A VAL 86 n 86 VAL 86 A GLY 87 n 87 GLY 87 A GLU 88 n 88 GLU 88 A PHE 89 n 89 PHE 89 A SER 90 n 90 SER 90 A GLY 91 n 91 GLY 91 A ALA 92 n 92 ALA 92 A ASN 93 n 93 ASN 93 A LYS 94 n 94 LYS 94 A GLU 95 n 95 GLU 95 A LYS 96 n 96 LYS 96 A LEU 97 n 97 LEU 97 A GLU 98 n 98 GLU 98 A ALA 99 n 99 ALA 99 A THR 100 n 100 THR 100 A ILE 101 n 101 ILE 101 A ASN 102 n 102 ASN 102 A GLU 103 n 103 GLU 103 A LEU 104 n 104 LEU 104 A VAL 105 n 105 VAL 105 A PHE 1 n 1 PHE 1 B ARG 2 n 2 ARG 2 B PHE 3 n 3 PHE 3 B ARG 4 n 4 ARG 4 B TYR 5 n 5 TYR 5 B VAL 6 n 6 VAL 6 B CYS 7 n 7 CYS 7 B GLU 8 n 8 GLU 8 B GLY 9 n 9 GLY 9 B PRO 10 n 10 PRO 10 B SER 11 n 11 SER 11 B HIS 12 n 12 HIS 12 B GLY 13 n 13 GLY 13 B author_defined_assembly 2 dimeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A O LYS 3 A O LYS 3 A N PHE 54 A N PHE 54 A O ILE 53 A O ILE 53 A N VAL 24 A N VAL 24 A O VAL 23 A O VAL 23 A N PHE 80 A N PHE 80 A O PHE 77 A O PHE 77 A N PHE 89 A N PHE 89 1 B B HD1 H HIS GLY 12 13 1.31 1 A PRO 40 -66.83 2.66 1 A PHE 41 -118.48 -76.17 1 A SER 90 -104.12 -168.12 1 A ALA 92 -57.57 95.87 1 B ARG 4 -136.44 -97.77 1 B TYR 5 -117.31 -167.56 1 B GLU 8 -82.78 43.23 1 B PRO 10 -66.74 23.12 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN MUTANT HUMAN THIOREDOXIN AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN NFKB 1 N N 2 N N 3 N N A LYS 8 A LYS 8 HELX_P A ALA 17 A ALA 17 1 1 10 A GLY 33 A GLY 33 HELX_P A PHE 42 A PHE 42 1 2 10 A SER 44 A SER 44 HELX_P A LYS 48 A LYS 48 5 3 5 A GLN 63 A GLN 63 HELX_P A ALA 69 A ALA 69 1 4 7 A LYS 94 A LYS 94 HELX_P A LEU 104 A LEU 104 1 5 11 disulf 2.023 A CYS 32 A SG CYS 32 1_555 B CYS 7 B SG CYS 7 1_555 COMPLEX (ELECTRON TRANSPORT/PEPTIDE) COMPLEX (ELECTRON TRANSPORT-PEPTIDE), COMPLEX (ELECTRON TRANSPORT-PEPTIDE) complex A THR 74 A THR 74 1 A PRO 75 A PRO 75 -1.61 THIO_HUMAN UNP 1 1 P10599 VKQIESKTAFQEALDAAGDKLVVVDFSATWCGPCKMIKPFFHSLSEKYSNVIFLEVDVDDCQDVASECEVKCMPTFQFFK KGQKVGEFSGANKEKLEATINELV NFKB1_HUMAN UNP 2 1 P19838 MADDDPYGTGQMFHLNTALTHSIFNAELYSPEIPLSTDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYP QVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACI RGYNPGLLVHSDLAYLQAEGGGDRQLTDREKEIIRQAAVQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDS KAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDVN ITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGSTGSPGP GYGYSNYGFPPYGGITFHPGVTKSNAGVTHGTINTKFKNGPKDCAKSDDEESLTLPEKETEGEGPSLPMACTKTEPIALA STMEDKEQDMGFQDNLFLEKALQLARRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHAQLVRDLLE VTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRVGADLSLLDRWGNSVLHLAAKEGHDRILSILLKSRKAAPLI DHPNGEGLNAIHIAVMSNSLPCLLLLVAAGAEVNAQEQKSGRTPLHLAVEYDNISLAGCLLLEGDAHVDSTTYDGTTPLH IAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWEKAGEDEGVVPGTTPLDMAANWQVFDILNGKPYEPVFTSDDILP QGDMKQLTEDTRLQLCKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTIKELMEALQQMGYTEA IEVIQAAFRTPATTASSPVTTAQVHCLPLSSSSTRQHIDELRDSDSVCDSGVETSFRKLSFTESLTGDSPLLSLNKMPHG YGQEGPIEGKI 1 104 1MDI 2 105 P10599 A 1 2 105 53 65 1MDI 1 13 P19838 B 2 1 13 1 CYS conflict ALA 35 1MDI A P10599 UNP 34 35 1 CYS conflict ALA 62 1MDI A P10599 UNP 61 62 1 CYS conflict ALA 69 1MDI A P10599 UNP 68 69 1 CYS conflict ALA 73 1MDI A P10599 UNP 72 73 1 MET conflict THR 74 1MDI A P10599 UNP 73 74 5 parallel parallel anti-parallel anti-parallel A VAL 2 A VAL 2 A ILE 5 A ILE 5 A ILE 53 A ILE 53 A VAL 57 A VAL 57 A VAL 23 A VAL 23 A PHE 27 A PHE 27 A THR 76 A THR 76 A LYS 81 A LYS 81 A GLN 84 A GLN 84 A SER 90 A SER 90 1 P 1