9dfd

;Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with lasso peptide lariocidin B, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.60A resolution ;

Method: X-RAY DIFFRACTION D_max: 374.8 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9dfd
沉积日期 deposition_date	2024-08-29
最后修订 last_revision	2024-11-20
结构标题 title	;Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with lasso peptide lariocidin B, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.60A resolution ;
关键词 keywords	Lasso peptide; RiPP; ribosome; antibiotic; tRNA; decoding; translocation; inhibitor; drug resistance, RIBOSOME; RIBOSOME
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	— Å
回转半径 Rg (电子) rg_electron	135.40 Å
零角强度 I(0) i0	902490000000.00
分子量 molecular_weight	4209100.0 kDa
排除体积 excluded_volume	3440900 Å³
包络体积 envelope_volume	8499800 Å³
水化壳体积 shell_volume	508760 Å³
包络直径 envelope_diameter	475.0 Å
壳层 Rg shell_rg	127.90 Å
包络 Rg envelope_rg	133.30 Å
形状 Rg shape_rg	135.70 Å
总 Rg total_rg	135.10 Å
总原子数 total_atoms	296198
残基数 n_residues	20910
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	374.8 Å
Rg (实空间) rg_real	128.90 Å
Rg 误差 (实空间) rg_real_error	1.61 Å
I(0) (实空间) i0_real	8.6670e+11
I(0) 误差 (实空间) i0_real_error	2.1340e+10
Rg (倒空间) rg_reciprocal	118.20 Å
I(0) (倒空间) i0_reciprocal	848200000000.0000
解质量估计 total_estimate	0.9055
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	136.3 Å
偏度 Skewness skewness	0.364
峰度 Kurtosis kurtosis	-0.719
角度范围 angular_range	— – 0.0550 Å⁻¹
当前正则化参数 α current_alpha	1.0360
最高正则化参数 α highest_alpha	14160000000.0000
实空间数据点数 n_real_points	12
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.002; Oscil: 0.974; Stabil: 0.972; Sysdev: 1.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.000

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (62)

Entity 1 polymer

描述 description	23S Ribosomal RNA
分子量 formula_weight	948007.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	1A,2A
原子数 atom_count	300583

GUCAAGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGCUACCUGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGGGGAACCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUGCGCGGGGGGAACCUGGGGAACUGAAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAGCGAAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGACACCGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCCGUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCAUGGGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCACCAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAACCGUGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCGAGUCCGAACAGGGCGCAAGCGGGCCGCACGCGGCCCGCAAAGUCCGCGGCCGUGGACCCGAAACCGGGCGAGCUAGCCCUGGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGAACCGGUGGGGGAUGCAAACCCCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAGCCCGGAGAUAGCUGGUUCUCCCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGGGCCUGUAGAGCACUGAUAGGGCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCCGAAGGGUCCCAGGUGGAGCCUGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCGCGGGAACAACCGAGACCGCCAGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGUGGCGCCGCGAAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGGCGCCGCGCCGAAAAUGAUCGGGGCUUAAGCCCAGCGCCGAAGCUGCGGGUCUGGGGGAUGACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGGCGGCUGGAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAAAGAGGGUGAGAAUCCCUCUCGCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGUAGGGUUAGGCGGGACCUAAGGUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUAUUCCGGCCCUUCCCGCAGGUGCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAUGGACGAGCCCGGCCAGAAGCGCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAACAAGCUCUGCGUGGUGGGGAAGCCCGUACGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGCCUCUAAGCACAACCUGCGGGAACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGAGCACUCAGGCGCGCGGGAGAACCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUCGGGAGAAGGGGUGCUCCCUGGGGUGAUGAGCCCCGGGGAGCCGCAGUGAACAGGCUCUGGCGACUGUUUACCAAAAACACAGCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGACGCUUGCCCGGUGCCGGAAGGUCAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAAGCGUAACGACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGAACUGGCCGUGAAGAUGCGGCCUACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACUGCAGCCUGGUGUUGGCUCUUGGUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAACCCUCGGAUGGGGGGACAGCGCUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAGGGUAGAAGGGGGCCUGACUGCGAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAGUGAACCGGUGGUCCCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGCGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCAGGAGGCUUGAGGGGGGCUCUUCCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUUCCCAGCUGUCCCUCCAGGGGCAUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCCGCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAGGACCCGGGAAGACCACCCGGUGGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCCGACCGGUCCCAAUCGUCCGAGGUCUUGACCCCUCC

Entity 2 polymer

描述 description	5S Ribosomal RNA
分子量 formula_weight	39188.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	1B,2B

UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAACGCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGAU

Entity 3 polymer

描述 description	50S ribosomal protein L2
分子量 formula_weight	30532.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1D,2D

MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK

Entity 4 polymer

描述 description	50S ribosomal protein L3
分子量 formula_weight	22450.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1E,2E

MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRETKKAAK

Entity 5 polymer

描述 description	50S ribosomal protein L4
分子量 formula_weight	23271.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1F,2F

MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNRIGGEA

Entity 6 polymer

描述 description	50S ribosomal protein L5
分子量 formula_weight	21061.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1G,2G

MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFRK

Entity 7 polymer

描述 description	50S ribosomal protein L6
分子量 formula_weight	19568.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1H,2H

MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERRHKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEGITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK

Entity 8 polymer

描述 description	50S ribosomal protein L9
分子量 formula_weight	16422.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1I,2I

MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAERKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPIKELGEYVLTYKPHPEVPIQLKVSVVAQE

Entity 9 polymer

描述 description	50S ribosomal protein L13
分子量 formula_weight	15927.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1N,2N

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV

Entity 10 polymer

描述 description	50S ribosomal protein L14
分子量 formula_weight	13323.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1O,2O

MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKAVVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPEVL

Entity 11 polymer

描述 description	50S ribosomal protein L15
分子量 formula_weight	16319.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1P,2P

MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLMRLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAGLLKKGYRLKILGEGEAKPLKVVAHAFSKSALEKLKAAGGEPVLLEA

Entity 12 polymer

描述 description	50S ribosomal protein L16
分子量 formula_weight	15993.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1Q,2Q

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAARVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPGRVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

Entity 13 polymer

描述 description	50S ribosomal protein L17
分子量 formula_weight	13750.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1R,2R

MRHLKSGRKLNRHSSHRLALYRNQAKSLLTHGRITTTVPKAKELRGFVDHLIHLAKRGDLHARRLVLRDLQDVKLVRKLFDEIAPRYRDRQGGYTRVLKLAERRRGDGAPLALVELVE

Entity 14 polymer

描述 description	50S ribosomal protein L18
分子量 formula_weight	12639.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1S,2S

MARLTAYERRKFRVRNRIKRTGRLRLSVFRSLKHIYAQIIDDEKGVTLVSASSLALKLKGNKTEVARQVGRALAEKALALGIKQVAFDRGPYKYHGRVKALAEGAREGGLEF

Entity 15 polymer

描述 description	50S ribosomal protein L19
分子量 formula_weight	17188.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1T,2T

MNRGALIKLVESRYVRTDLPEFRPGDTVRVSYKVKEGNRTRIQDFEGIVIRIRRNGFNTTFTVRKVSYGVGVERIFPLHSPLIQKIDIVQRGRARRAKLYFIRNLSDREIRRKLRADRKRIDQDRAAERAAKEEAQKAQEPKASQE

Entity 16 polymer

描述 description	50S ribosomal protein L20
分子量 formula_weight	13779.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1U,2U

MPRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRKRRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVREPQVFAELVERAKAAQG

Entity 17 polymer

描述 description	50S ribosomal protein L21
分子量 formula_weight	11069.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1V,2V

MFAIVKTGGKQYRVEPGLKLRVEKLDAEPGATVELPVLLLGGEKTVVGTPVVEGASVVAEVLGHGRGKKILVSKFKAKVQYRRKKGHRQPYTELLIKEIRG

Entity 18 polymer

描述 description	50S ribosomal protein L22
分子量 formula_weight	12808.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1W,2W

MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKVLESAAANAVNNHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRTSHITVILGEKHGK

Entity 19 polymer

描述 description	50S ribosomal protein L23
分子量 formula_weight	10759.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1X,2X

MKTAYDVILAPVLSEKAYAGFAEGKYTFWVHPKATKTEIKNAVETAFKVKVVKVNTLHVRGKKKRLGRYLGKRPDRKKAIVQVAPGQKIEALEGLI

Entity 20 polymer

描述 description	50S ribosomal protein L24
分子量 formula_weight	12085.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1Y,2Y

MRVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGKKIRVCAKCGGALDTEE

Entity 21 polymer

描述 description	50S ribosomal protein L25
分子量 formula_weight	23238.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1Z,2Z

MEYRLKAYYREGEKPSALRRAGKLPGVMYNRHLNRKVYVDLVEFDKVFRQASIHHVIVLELPDGQSLPTLVRQVNLDKRRRRPEHVDFFVLSDEPVEMYVPLRFVGTPAGVRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVVPPEDVEKLAEEAAAEVAEPEVIKKGKEEEEE

Entity 22 polymer

描述 description	50S ribosomal protein L27
分子量 formula_weight	9529.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	10,20

MAHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPLA

Entity 23 polymer

描述 description	50S ribosomal protein L28
分子量 formula_weight	11004.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	11,21

MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVAGQEITFRVAASHIPKVYELVERAKGLKLEGLSPKEIKKELLKLL

Entity 24 polymer

描述 description	50S ribosomal protein L29
分子量 formula_weight	8670.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	12,22

MKLSEVRKQLEEARKLSPVELEKLVREKKRELMELRFQASIGQLSQNHKIRDLKRQIARLLTVLNEKRRQNA

Entity 25 polymer

描述 description	50S ribosomal protein L30
分子量 formula_weight	6799.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	13,23

MPRLKVKLVKSPIGYPKDQKAALKALGLRRLQQERVLEDTPAIRGNVEKVAHLVRVEVVE

Entity 26 polymer

描述 description	50S ribosomal protein L31
分子量 formula_weight	8300.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	14,24

MKEGIHPKLVPARIICGCGNVIETYSTKPEIYVEVCSKCHPFYTGQQRFVDTEGRVERFQRRYGDSYRKGR

Entity 27 polymer

描述 description	50S ribosomal protein L32
分子量 formula_weight	6722.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	15,25

MAKHPVPKKKTSKARRDARRSHHALTPPTLVPCPECKAMKPPHTVCPECGYYAGRKVLEV

Entity 28 polymer

描述 description	50S ribosomal protein L33
分子量 formula_weight	6632.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	16,26

MASEVRIKLLLECTECKRRNYATEKNKRNTPNKLELRKYCPWCRKHTVHREVKI

Entity 29 polymer

描述 description	50S ribosomal protein L34
分子量 formula_weight	6132.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	17,27

MKRTWQPNRRKRAKTHGFRARMRTPGGRKVLKRRRQKGRWRLTPAVRKR

Entity 30 polymer

描述 description	50S ribosomal protein L35
分子量 formula_weight	7506.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	18,28

MPKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKLLLPYE

Entity 31 polymer

描述 description	50S ribosomal protein L36
分子量 formula_weight	4435.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	19,29

MKVRASVKRICDKCKVIRRHGRVYVICENPKHKQRQG

Entity 32 polymer

描述 description	16S Ribosomal RNA
分子量 formula_weight	493863.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	1a,2a

UUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU

Entity 33 polymer

描述 description	30S ribosomal protein S2
分子量 formula_weight	29317.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1b,2b

MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQEAEATETPEGESEVEA

Entity 34 polymer

描述 description	30S ribosomal protein S3
分子量 formula_weight	26751.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1c,2c

MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Entity 35 polymer

描述 description	30S ribosomal protein S4
分子量 formula_weight	24373.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1d,2d

MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR

Entity 36 polymer

描述 description	30S ribosomal protein S5
分子量 formula_weight	17583.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1e,2e

MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Entity 37 polymer

描述 description	30S ribosomal protein S6
分子量 formula_weight	11988.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1f,2f

MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Entity 38 polymer

描述 description	30S ribosomal protein S7
分子量 formula_weight	18051.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1g,2g

MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Entity 39 polymer

描述 description	30S ribosomal protein S8
分子量 formula_weight	15868.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1h,2h

MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW

Entity 40 polymer

描述 description	30S ribosomal protein S9
分子量 formula_weight	14410.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1i,2i

MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR

Entity 41 polymer

描述 description	30S ribosomal protein S10
分子量 formula_weight	11955.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1j,2j

MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Entity 42 polymer

描述 description	30S ribosomal protein S11
分子量 formula_weight	13737.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1k,2k

MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS

Entity 43 polymer

描述 description	30S ribosomal protein S12
分子量 formula_weight	14683.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1l,2l

MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKXLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEAAKTAAKK

Entity 44 polymer

描述 description	30S ribosomal protein S13
分子量 formula_weight	14338.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1m,2m

MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK

Entity 45 polymer

描述 description	30S ribosomal protein S14 type Z
分子量 formula_weight	7158.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1n,2n

MARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW

Entity 46 polymer

描述 description	30S ribosomal protein S15
分子量 formula_weight	10578.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1o,2o

MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG

Entity 47 polymer

描述 description	30S ribosomal protein S16
分子量 formula_weight	10410.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1p,2p

MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVFRQEAREGA

Entity 48 polymer

描述 description	30S ribosomal protein S17
分子量 formula_weight	12325.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1q,2q

MPKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYESLSKRGGKA

Entity 49 polymer

描述 description	30S ribosomal protein S18
分子量 formula_weight	10258.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1r,2r

MSTKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLPFTEKLVRK

Entity 50 polymer

描述 description	30S ribosomal protein S19
分子量 formula_weight	10605.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1s,2s

MPRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHGKEAKATKKK

Entity 51 polymer

描述 description	30S ribosomal protein S20
分子量 formula_weight	11736.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1t,2t

MAQKKPKRNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAIQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARRKSRLMRKVRQLLEAAGAPLIGGGLSA

Entity 52 polymer

描述 description	30S ribosomal protein Thx
分子量 formula_weight	3350.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1u,2u

MGKGDRRTRRGKIWRGTYGKYRPRKKK

Entity 53 polymer

描述 description	MET-PHE-mRNA
分子量 formula_weight	7804.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	1v,2v

GGCAAGGAGGUAAAAAUGUUCUAA

Entity 54 polymer

描述 description	A-site Aminoacylated Phe-tRNAphe
分子量 formula_weight	24791.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	1w,2w

GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGGGCACCX

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 55 polymer

描述 description	P-site Aminoacylated fMet-tRNAmet
分子量 formula_weight	25005.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	1x,2x

CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAUCCGGCCCCCGCAACCX

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 56 polymer

描述 description	E-site Deacylated tRNAphe
分子量 formula_weight	24644.9 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	1y,2y

GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGGGCACCA

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 57 polymer

描述 description	Lasso peptide lariocidin B
分子量 formula_weight	1839.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1z,2z

SKKSKPGDGKFGRGVKR

来源 Source

来源生物 organism	Paenibacillus
NCBI 分类编号 ncbi_taxonomy_id	44249
宿主生物 host_organism	Streptomyces lividans

Entity 58 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2804

Entity 59 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 60 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 61 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 62 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	4385

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	210.290 Å
晶胞边长 b length_b	450.050 Å
晶胞边长 c length_c	626.340 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	365.480 Å
R 因子 r_factor	0.2175
R_work r_work	0.2149
R_free r_free	0.2658

fit	/app/data/saxs_computation/df/9dfd/9dfd.fit
pddf	/app/data/pr_computation/df/9dfd/9dfd.pr.out
profile	/app/data/saxs_computation/df/9dfd/9dfd.dat

;Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with lasso peptide lariocidin B, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.60A resolution ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (62)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

Entity 11 polymer

聚合体 Polymer

Entity 12 polymer

聚合体 Polymer

Entity 13 polymer

聚合体 Polymer

Entity 14 polymer

聚合体 Polymer

Entity 15 polymer

聚合体 Polymer

Entity 16 polymer

聚合体 Polymer

Entity 17 polymer

聚合体 Polymer

Entity 18 polymer

聚合体 Polymer

Entity 19 polymer

聚合体 Polymer

Entity 20 polymer

聚合体 Polymer

Entity 21 polymer

聚合体 Polymer

Entity 22 polymer

聚合体 Polymer

Entity 23 polymer

聚合体 Polymer

Entity 24 polymer

聚合体 Polymer

Entity 25 polymer

聚合体 Polymer

Entity 26 polymer

聚合体 Polymer

Entity 27 polymer

聚合体 Polymer

Entity 28 polymer

聚合体 Polymer

Entity 29 polymer

聚合体 Polymer

Entity 30 polymer

聚合体 Polymer

Entity 31 polymer

聚合体 Polymer

Entity 32 polymer

聚合体 Polymer

Entity 33 polymer

聚合体 Polymer

Entity 34 polymer

聚合体 Polymer