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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5TGM

Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1218S ribosomal RNApolymer1812583803.71Saccharomyces cerevisiae
2S0, s040S ribosomal protein S0-Apolymer20622811.12UniProt (B3LI22)
Pfam (PF00318)
UniProt (by SIFTS) (P32905)
In PDB		Saccharomyces cerevisiae (baker's yeast)Nucleic acid-binding protein NAB1A
3S1, s140S ribosomal protein S1-Bpolymer21624498.42UniProt (P23248)
Pfam (PF01015)
UniProt (by SIFTS) (P33442)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP10B,Small ribosomal subunit protein eS1-B
4S2, s240S ribosomal protein S2polymer21723213.02UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
In PDB		Saccharomyces cerevisiae (baker's yeast)Omnipotent suppressor protein SUP44,RP12,S4,Small ribosomal subunit protein uS5,YS5
5S3, s340S ribosomal protein S3polymer22324702.82UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP13,Small ribosomal subunit protein uS3,YS3
6S4, s440S ribosomal protein S4-Apolymer26029338.12UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP5,S7,Small ribosomal subunit protein eS4-A,YS6
7S5, s540S ribosomal protein S5polymer20622908.32UniProt (P26783)
Pfam (PF00177)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP14,S2,Small ribosomal subunit protein uS7,YS8
8S6, s640S ribosomal protein S6-Apolymer22625895.12UniProt (P0CX37)
Pfam (PF01092)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP9,S10,Small ribosomal subunit protein eS6-A,YS4
9S7, s740S ribosomal protein S7-Apolymer18621158.62UniProt (P26786)
Pfam (PF01251)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP30,RP40,Small ribosomal subunit protein eS7-A
10S8, s840S ribosomal protein S8-Apolymer19922406.62UniProt (P0CX39)
Pfam (PF01201)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP19,S14,Small ribosomal subunit protein eS8-A,YS9
11S9, s940S ribosomal protein S9-Apolymer18521210.72UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP21,S13,Small ribosomal subunit protein uS4-A,YP28,YS11
12C0, c040S ribosomal protein S10-Apolymer10512757.42UniProt (Q08745)
Pfam (PF03501)
In PDB		Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein eS10-A
13C1, c140S ribosomal protein S11-Apolymer15617785.92UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP41,S18,Small ribosomal subunit protein uS17-A,YS12
14C2, c240S ribosomal protein S12polymer14315488.62UniProt (P48589)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein eS12
15C3, c340S ribosomal protein S13polymer15016928.72UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
In PDB		Saccharomyces cerevisiae (baker's yeast)S27a,Small ribosomal subunit protein uS15,YS15
16C4, c440S ribosomal protein S14-Bpolymer12813560.52UniProt (P39516)
Pfam (PF00411)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP59B,Small ribosomal subunit protein uS11-B
17C5, c540S ribosomal protein S15polymer14216031.92UniProt (Q01855)
Pfam (PF00203)
In PDB		Saccharomyces cerevisiae (baker's yeast)RIG protein,RP52,S21,Small ribosomal subunit protein uS19,YS21
18C6, c640S ribosomal protein S16-Apolymer14215746.32UniProt (P0CX51)
Pfam (PF00380)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP61R,Small ribosomal subunit protein uS9-A
19C7, c740S ribosomal protein S17-Bpolymer12514268.52UniProt (P14127)
Pfam (PF00833)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP51B,Small ribosomal subunit protein eS17-B
20C8, c840S ribosomal protein S18-Apolymer14516940.42UniProt (P0CX55)
Pfam (PF00416)
In PDB		Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein uS13-A
21C9, c940S ribosomal protein S19-Apolymer14315810.92UniProt (P07280)
Pfam (PF01090)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP55A,S16a,Small ribosomal subunit protein eS19-A,YP45,YS16A
22D0, d040S ribosomal protein S20polymer11012575.52UniProt (P38701)
Pfam (PF00338)
In PDB		Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein uS10
23D1, d140S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)
In PDB		Saccharomyces cerevisiae (baker's yeast)S26,Small ribosomal subunit protein eS21-A,YS25
24D2, d240S ribosomal protein S22-Apolymer12914518.92UniProt (P0C0W1)
Pfam (PF00410)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP50,S24,Small ribosomal subunit protein uS8-A,YP58,YS22
25D3, d340S ribosomal protein S23-Apolymer14415942.72UniProt (P0CX29)
Pfam (PF00164)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP37,S28,Small ribosomal subunit protein uS12-A,YS14
26D4, d440S ribosomal protein S24-Apolymer13415231.62UniProt (P0CX31)
Pfam (PF01282)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP50,Small ribosomal subunit protein eS24-A
27D5, d540S ribosomal protein S25-Apolymer708001.42UniProt (Q3E792)
Pfam (PF03297)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP45,S31,Small ribosomal subunit protein eS25-A,YS23
28D6, d640S ribosomal protein S26-Bpolymer9711023.02UniProt (P39939)
Pfam (PF01283)
In PDB		Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein eS26-B
29D7, d740S ribosomal protein S27-Apolymer818762.22UniProt (P35997)
Pfam (PF01667)
In PDB		Saccharomyces cerevisiae (baker's yeast)RP61,Small ribosomal subunit protein eS27-A,YS20
30D8, d840S ribosomal protein S28-Apolymer637116.32UniProt (Q3E7X9)
Pfam (PF01200)
In PDB		Saccharomyces cerevisiae (baker's yeast)S33,Small ribosomal subunit protein eS28-A,YS27
31D9, d940S ribosomal protein S29-Apolymer536335.32UniProt (P41057)
Pfam (PF00253)
In PDB		Saccharomyces cerevisiae (baker's yeast)S36,Small ribosomal subunit protein uS14-A,YS29
32E0, e040S ribosomal protein S30-Apolymer627006.32UniProt (P0CX33)
Pfam (PF04758)
In PDB		Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein eS30-A
33E1, e140S ribosomal protein S31polymer768703.52UniProt (P05759)
Pfam (PF01599)
In PDB		Saccharomyces cerevisiae (baker's yeast)CEP76,S37,Small ribosomal subunit protein eS31,YS24
34SRGuanine nucleotide-binding protein subunit beta-like proteinpolymer31834651.91UniProt (P38011)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (baker's yeast)Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1,Small ribosomal subunit protein RACK1
35SMSuppressor protein STM1,Ribosome-bound protein Stm1,Suppressor protein STM1,Ribosome-bound protein Stm1polymer29932258.81UniProt (P39015)
Pfam (PF09598)
In PDB		Saccharomyces cerevisiae (baker's yeast)3BP1,GU4 nucleic-binding protein 2,G4p2 protein,POP2 multicopy suppressor protein 4,Ribosomal subunits association factor,AF,TOM1 suppressor protein 1,Triplex-binding protein 1
36125S ribosomal RNApolymer31491017859.11Saccharomyces cerevisiae
373, 75S ribosomal RNApolymer12138951.12GenBank (1039024045)Saccharomyces cerevisiae (baker's yeast)
384, 85.8S ribosomal RNApolymer15850682.92GenBank (1331532632)Saccharomyces cerevisiae (baker's yeast)
39L2, l260S ribosomal protein L2-Apolymer25227217.32UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
In PDB		Saccharomyces cerevisiae (baker's yeast)L5,Large ribosomal subunit protein uL2-A,RP8,YL6
40L3, l360S ribosomal protein L3polymer38643719.62UniProt (P14126)
Pfam (PF00297)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
41L4, l460S ribosomal protein L4-Apolymer36139027.92UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
In PDB		Saccharomyces cerevisiae (baker's yeast)L2,Large ribosomal subunit protein uL4-A,RP2,YL2
42L5, l560S ribosomal protein L5polymer29633633.62UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
In PDB		Saccharomyces cerevisiae (baker's yeast)L1,L1a,Large ribosomal subunit protein uL18,Ribosomal 5S RNA-binding protein,YL3
43L6, l660S ribosomal protein L6-Apolymer17519869.42UniProt (Q02326)
Pfam (PF01159)
In PDB		Saccharomyces cerevisiae (baker's yeast)L17,Large ribosomal subunit protein eL6-A,RP18,YL16
44L7, l760S ribosomal protein L7-Apolymer22325341.52UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
In PDB		Saccharomyces cerevisiae (baker's yeast)L6,Large ribosomal subunit protein uL30-A,RP11,YL8
45L860S ribosomal protein L8-Apolymer23325815.01UniProt (P17076)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (baker's yeast)L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5
46L9, l960S ribosomal protein L9-Apolymer19121605.12UniProt (P05738)
Pfam (PF00347)
In PDB		Saccharomyces cerevisiae (baker's yeast)L8,Large ribosomal subunit protein uL6-A,RP24,YL11
47M0, m060S ribosomal protein L10polymer22025279.32UniProt (P41805)
Pfam (PF00252)
In PDB		Saccharomyces cerevisiae (baker's yeast)L9,Large ribosomal subunit protein uL16,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
48M1, m160S ribosomal protein L11-Bpolymer16919266.12UniProt (Q3E757)
Pfam (PF00281)
Pfam (PF00673)
In PDB		Saccharomyces cerevisiae (baker's yeast)L16,Large ribosomal subunit protein uL5-B,RP39,YL22
49M3, m360S ribosomal protein L13-Apolymer19421956.32UniProt (Q12690)
Pfam (PF01294)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL13-A
50M4, m460S ribosomal protein L14-Apolymer13715063.92UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL14-A
51M5, m560S ribosomal protein L15-Apolymer20324351.22UniProt (P05748)
Pfam (PF00827)
In PDB		Saccharomyces cerevisiae (baker's yeast)L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18
52M6, m660S ribosomal protein L16-Apolymer19722029.02UniProt (P26784)
Pfam (PF00572)
In PDB		Saccharomyces cerevisiae (baker's yeast)L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15
53M7, m760S ribosomal protein L17-Apolymer18320458.32UniProt (P05740)
Pfam (PF00237)
In PDB		Saccharomyces cerevisiae (baker's yeast)L20A,Large ribosomal subunit protein uL22-A,YL17
54M8, m860S ribosomal protein L18-Apolymer18520478.12UniProt (P0CX49)
Pfam (PF17135)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL18-A,RP28
55M9, m960S ribosomal protein L19-Apolymer18821631.12UniProt (P0CX82)
Pfam (PF01280)
In PDB		Saccharomyces cerevisiae (baker's yeast)L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14
56N0, n060S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)
In PDB		Saccharomyces cerevisiae (baker's yeast)L18a,Large ribosomal subunit protein eL20-A
57N1, n160S ribosomal protein L21-Apolymer15918148.12UniProt (Q02753)
Pfam (PF01157)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL21-A
58N2, n260S ribosomal protein L22-Apolymer10011263.92UniProt (P05749)
Pfam (PF01776)
In PDB		Saccharomyces cerevisiae (baker's yeast)L1c,Large ribosomal subunit protein eL22-A,RP4,YL31
59N3, n360S ribosomal protein L23-Apolymer13614362.82UniProt (P0CX41)
Pfam (PF00238)
In PDB		Saccharomyces cerevisiae (baker's yeast)L17a,Large ribosomal subunit protein uL14-A,YL32
60N460S ribosomal protein L24-Apolymer9811369.41UniProt (P04449)
Pfam (PF01246)
In PDB		Saccharomyces cerevisiae (baker's yeast)L30,Large ribosomal subunit protein eL24-A,RP29,YL21
61N5, n560S ribosomal protein L25polymer12113771.22UniProt (P04456)
Pfam (PF00276)
Pfam (PF03939)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein uL23,RP16L,YL25,YP42'
62N6, n660S ribosomal protein L26-Apolymer12614134.62UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
In PDB		Saccharomyces cerevisiae (baker's yeast)L33,Large ribosomal subunit protein uL24-A,YL33
63N7, n760S ribosomal protein L27-Apolymer13515437.22UniProt (P0C2H6)
Pfam (PF01777)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL27-A
64N8, n860S ribosomal protein L28polymer14816630.52UniProt (P02406)
Pfam (PF00828)
In PDB		Saccharomyces cerevisiae (baker's yeast)L27a,L29,Large ribosomal subunit protein uL15,RP44,RP62,YL24
65N9, n960S ribosomal protein L29polymer586560.72UniProt (P05747)
Pfam (PF01779)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL29,YL43
66O0, o060S ribosomal protein L30polymer10010902.72UniProt (P14120)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (baker's yeast)L32,Large ribosomal subunit protein eL30,RP73,YL38
67O1, o160S ribosomal protein L31-Apolymer10912649.82UniProt (P0C2H8)
Pfam (PF01198)
In PDB		Saccharomyces cerevisiae (baker's yeast)L34,Large ribosomal subunit protein eL31-A,YL28
68O2, o260S ribosomal protein L32polymer12714478.12UniProt (P38061)
Pfam (PF01655)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL32
69O3, o360S ribosomal protein L33-Apolymer10612045.92UniProt (P05744)
Pfam (PF01247)
In PDB		Saccharomyces cerevisiae (baker's yeast)L37,Large ribosomal subunit protein eL33-A,RP47,YL37
70O4, o460S ribosomal protein L34-Apolymer11212608.82UniProt (P87262)
Pfam (PF01199)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL34-A
71O5, o560S ribosomal protein L35-Apolymer11913811.42UniProt (P0CX84)
Pfam (PF00831)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein uL29-A
72O6, o660S ribosomal protein L36-Apolymer9911020.12UniProt (P05745)
Pfam (PF01158)
In PDB		Saccharomyces cerevisiae (baker's yeast)L39,Large ribosomal subunit protein eL36-A,YL39
73O7, o760S ribosomal protein L37-Apolymer879746.22UniProt (P49166)
Pfam (PF01907)
In PDB		Saccharomyces cerevisiae (baker's yeast)L43,Large ribosomal subunit protein eL37-A,YL35,YP55
74O8, o860S ribosomal protein L38polymer778714.42UniProt (P49167)
Pfam (PF01781)
In PDB		Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL38
75O9, o960S ribosomal protein L39polymer506227.42UniProt (P04650)
Pfam (PF00832)
In PDB		Saccharomyces cerevisiae (baker's yeast)L46,Large ribosomal subunit protein eL39,YL40
76Q0, q060S ribosomal protein L40-Apolymer526032.32UniProt (P0CH08)
Pfam (PF01020)
In PDB		Saccharomyces cerevisiae (baker's yeast)CEP52,Large ribosomal subunit protein eL40-A
77Q1, q160S ribosomal protein L41-Apolymer253354.22UniProt (P0CX86)
Pfam (PF05162)
In PDB		Saccharomyces cerevisiae (baker's yeast)L47,Large ribosomal subunit protein eL41-A,YL41
78Q2, q260S ribosomal protein L42-Apolymer10512115.52UniProt (P0CX27)
Pfam (PF00935)
In PDB		Saccharomyces cerevisiae (baker's yeast)L41,Large ribosomal subunit protein eL42-A,YL27,YP44
79Q3, q360S ribosomal protein L43-Apolymer919981.82UniProt (P0CX25)
Pfam (PF01780)
In PDB		Saccharomyces cerevisiae (baker's yeast)L37a,Large ribosomal subunit protein eL43-A,YL35
80618S ribosomal RNApolymer1800579761.91GenBank (874346701)Saccharomyces cerevisiae (baker's yeast)
81sRGuanine nucleotide-binding protein subunit beta-like proteinpolymer31834710.01UniProt (P38011)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (baker's yeast)Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1,Small ribosomal subunit protein RACK1
82sMSuppressor protein STM1polymer27330048.01UniProt (P39015)
Pfam (PF09598)
In PDB		Saccharomyces cerevisiae (baker's yeast)3BP1,GU4 nucleic-binding protein 2,G4p2 protein,POP2 multicopy suppressor protein 4,Ribosomal subunits association factor,AF,TOM1 suppressor protein 1,Triplex-binding protein 1
83525S ribosomal RNApolymer31501018196.41Saccharomyces cerevisiae
84l860S ribosomal protein L8-Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (baker's yeast)L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5
85m260S ribosomal protein L12-Apolymer16517850.61UniProt (P0CX53)
Pfam (PF03946)
Pfam (PF00298)
In PDB		Saccharomyces cerevisiae (baker's yeast)L15,Large ribosomal subunit protein uL11-A,YL23
86n460S ribosomal protein L24-Apolymer13515506.21UniProt (P04449)
Pfam (PF01246)
In PDB		Saccharomyces cerevisiae (baker's yeast)L30,Large ribosomal subunit protein eL24-A,RP29,YL21
87p060S acidic ribosomal protein P0polymer31233749.11UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Pfam (PF00428)
In PDB		Saccharomyces cerevisiae (baker's yeast)A0,L10e,Large ribosomal subunit protein uL10
88p1, p260S ribosomal protein L40-Apolymer12814583.12UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)
In PDB		Saccharomyces cerevisiae (baker's yeast)CEP52,Large ribosomal subunit protein eL40-A
89P, pPeptidyl-tRNA analog ACCA-Leu-Phepolymer41223.82Homo sapiens
901, 6, 2, 5, 8...osmium (III) hexamminenon-polymer286.41095Chemie (OHX)
915, 1, 6, c8, 2...MAGNESIUM IONnon-polymer24.31191Chemie (MG)
92D7, D9, E1, d6, O7...ZINC IONnon-polymer65.416Chemie (ZN)
931, 5PHENYLALANINEnon-polymer165.22Chemie (PHE)
941, 5LEUCINEnon-polymer131.22Chemie (LEU)
951, 5SPARSOMYCINnon-polymer361.42Chemie (SPS)
96p, P3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)non-polymer346.22Chemie (8AN)
Sequence modifications
S1, s1: 20 - 235 (UniProt: P23248)
PDBExternal DatabaseDetails
Ser 56Asn 56conflict
Ile 84Val 84conflict
Lys 174Arg 174conflict
Gly 178Asn 178conflict
SR: 2 - 319 (UniProt: P38011)
PDBExternal DatabaseDetails
Ala 161Lys 161conflict
SM: 1 - 146 (UniProt: P39015)
PDBExternal DatabaseDetails
Leu 134Asp 134conflict
SM: 151 - 176 (PDB: 5TGM)
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains164
Total formula weight6062320.5
Non-Polymers*Number of molecules2310
Total formula weight345571.5
All*Total formula weight6407892.1
*Water molecules are not included.

218196

건을2024-04-10부터공개중

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