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8CDR

Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(0)
40S ribosomal protein S24-Apolymer13515362.81UniProt (P0CX31)
Pfam (PF01282)
Saccharomyces cerevisiae (baker's yeast)RP50,Small ribosomal subunit protein eS24-A
2B
(1)
40S ribosomal protein S25-Apolymer10812067.31UniProt (Q3E792)
Pfam (PF03297)
Saccharomyces cerevisiae (baker's yeast)RP45,S31,Small ribosomal subunit protein eS25-A,YS23
3C
(2)
40S ribosomal protein S26polymer11913538.91UniProt (A0A6A5PUG0)
Pfam (PF01283)
UniProt (by SIFTS) (P39938)
Saccharomyces cerevisiae (baker's yeast)
4D
(3)
40S ribosomal protein S27-Apolymer828893.41UniProt (P35997)
Pfam (PF01667)
Saccharomyces cerevisiae (baker's yeast)RP61,Small ribosomal subunit protein eS27-A,YS20
5E
(4)
40S ribosomal protein S28-Apolymer677605.81UniProt (Q3E7X9)
Pfam (PF01200)
Saccharomyces cerevisiae (baker's yeast)S33,Small ribosomal subunit protein eS28-A,YS27
6F
(5)
HLJ1_G0030400.mRNA.1.CDS.1polymer566675.71UniProt (A0A6A5PV92)
Pfam (PF00253)
UniProt (by SIFTS) (P41057)
Saccharomyces cerevisiae (baker's yeast)HLJ1_G0038740.mRNA.1.CDS.1,HN1_G0030180.mRNA.1.CDS.1,JXXY16_1_G0039900.mRNA.1.CDS.1,SX2_G0030120.mRNA.1.CDS.1,XXYS1_4_G0042270.mRNA.1.CDS.1,Y55_G0030330.mRNA.1.CDS.1
7G
(6)
40S ribosomal protein S30-Apolymer637137.51UniProt (P0CX33)
Pfam (PF04758)
Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein eS30-A
8H
(7)
Guanine nucleotide-binding protein subunit beta-like proteinpolymer31934841.21UniProt (P38011)
Pfam (PF00400)
Saccharomyces cerevisiae (baker's yeast)Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1,Small ribosomal subunit protein RACK1
9I
(8)
Ubiquitin-40S ribosomal protein S31polymer15217254.21UniProt (A0A6A5PU37)
Pfam (PF00240)
Pfam (PF01599)
UniProt (by SIFTS) (P05759)
Saccharomyces cerevisiae (baker's yeast)
10J
(A)
60S ribosomal protein L16-Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)
Saccharomyces cerevisiae (baker's yeast)L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15
11K
(AA)
25S ribosomal RNApolymer33961098082.81GenBank (1262303)Saccharomyces cerevisiae (baker's yeast)
12L
(Aa)
Elongation factor 2polymer84293549.31UniProt (A0A6A5Q7K2)
Pfam (PF00009)
Pfam (PF03144)
Pfam (PF14492)
Pfam (PF03764)
Pfam (PF00679)
UniProt (by SIFTS) (P32324)
Saccharomyces cerevisiae (baker's yeast)
13M
(B)
60S ribosomal protein L17-Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)
Saccharomyces cerevisiae (baker's yeast)L20A,Large ribosomal subunit protein uL22-A,YL17
14N
(BB)
5S ribosomal RNApolymer12138951.11GenBank (1329886537)Saccharomyces cerevisiae (baker's yeast)
15O
(Bb)
Transfer RNA Phepolymer7624743.81GenBank (176419)Saccharomyces cerevisiae (baker's yeast)
16P
(C)
60S ribosomal protein L18-Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL18-A,RP28
17Q
(CC)
5.8S ribosomal RNApolymer15850682.91GenBank (1331532632)Saccharomyces cerevisiae (baker's yeast)
18R
(Cc)
Transfer RNA fMetpolymer7724801.81GenBank (170517292)Escherichia coli
19S
(D)
60S ribosomal protein L19-Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)
Saccharomyces cerevisiae (baker's yeast)L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14
20T
(DD)
60S acidic ribosomal protein P0polymer31233749.11UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Pfam (PF00428)
Saccharomyces cerevisiae (baker's yeast)A0,L10e,Large ribosomal subunit protein uL10
21U
(Dd)
Messenger RNApolymer3912744.81Saccharomyces cerevisiae
22V
(E)
60S ribosomal protein L20-Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)
Saccharomyces cerevisiae (baker's yeast)L18a,Large ribosomal subunit protein eL20-A
23W
(EE)
60S ribosomal protein L2-Apolymer25427463.61UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
Saccharomyces cerevisiae (baker's yeast)L5,Large ribosomal subunit protein uL2-A,RP8,YL6
24X
(Ee)
60S ribosomal protein L12-Apolymer16517850.61UniProt (P0CX53)
Pfam (PF03946)
Pfam (PF00298)
Saccharomyces cerevisiae (baker's yeast)L15,Large ribosomal subunit protein uL11-A,YL23
25Y
(F)
60S ribosomal protein L21-Apolymer16018279.31UniProt (Q02753)
Pfam (PF01157)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL21-A
26Z
(FF)
60S ribosomal protein L3polymer38743850.81UniProt (P14126)
Pfam (PF00297)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
27AA
(G)
60S ribosomal protein L22-Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)
Saccharomyces cerevisiae (baker's yeast)L1c,Large ribosomal subunit protein eL22-A,RP4,YL31
28BA
(GG)
60S ribosomal protein L4-Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
Saccharomyces cerevisiae (baker's yeast)L2,Large ribosomal subunit protein uL4-A,RP2,YL2
29CA
(H)
60S ribosomal protein L23-Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)
Saccharomyces cerevisiae (baker's yeast)L17a,Large ribosomal subunit protein uL14-A,YL32
30DA
(HH)
60S ribosomal protein L5polymer29733764.81UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
Saccharomyces cerevisiae (baker's yeast)L1,L1a,Large ribosomal subunit protein uL18,Ribosomal 5S RNA-binding protein,YL3
31EA
(I)
60S ribosomal protein L24-Apolymer15517661.71UniProt (P04449)
Pfam (PF01246)
Saccharomyces cerevisiae (baker's yeast)L30,Large ribosomal subunit protein eL24-A,RP29,YL21
32FA
(II)
60S ribosomal protein L6-Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)
Saccharomyces cerevisiae (baker's yeast)L17,Large ribosomal subunit protein eL6-A,RP18,YL16
33GA
(J)
60S ribosomal protein L25polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein uL23,RP16L,YL25,YP42'
34HA
(JJ)
60S ribosomal protein L7-Apolymer24427686.31UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
Saccharomyces cerevisiae (baker's yeast)L6,Large ribosomal subunit protein uL30-A,RP11,YL8
35IA
(K)
60S ribosomal protein L26-Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
Saccharomyces cerevisiae (baker's yeast)L33,Large ribosomal subunit protein uL24-A,YL33
36JA
(KK)
60S ribosomal protein L8-Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)
Saccharomyces cerevisiae (baker's yeast)L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5
37KA
(L)
60S ribosomal protein L27-Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL27-A
38LA
(LL)
60S ribosomal protein L9-Apolymer19121605.11UniProt (P05738)
Pfam (PF00347)
Saccharomyces cerevisiae (baker's yeast)L8,Large ribosomal subunit protein uL6-A,RP24,YL11
39MA
(M)
60S ribosomal protein L28polymer14916761.71UniProt (P02406)
Pfam (PF00828)
Saccharomyces cerevisiae (baker's yeast)L27a,L29,Large ribosomal subunit protein uL15,RP44,RP62,YL24
40NA
(MM)
60S ribosomal protein L10polymer22125410.51UniProt (P41805)
Pfam (PF00252)
Saccharomyces cerevisiae (baker's yeast)L9,Large ribosomal subunit protein uL16,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
41OA
(N)
60S ribosomal protein L29polymer596691.91UniProt (P05747)
Pfam (PF01779)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL29,YL43
42PA
(NN)
60S ribosomal protein L11-Apolymer17419755.71UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)
Saccharomyces cerevisiae (baker's yeast)L16,Large ribosomal subunit protein uL5-A,RP39,YL22
43QA
(O)
60S ribosomal protein L30polymer10511430.41UniProt (P14120)
Pfam (PF01248)
Saccharomyces cerevisiae (baker's yeast)L32,Large ribosomal subunit protein eL30,RP73,YL38
44RA
(OO)
60S ribosomal protein L13-Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL13-A
45SA
(P)
60S ribosomal protein L31-Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)
Saccharomyces cerevisiae (baker's yeast)L34,Large ribosomal subunit protein eL31-A,YL28
46TA
(PP)
60S ribosomal protein L14-Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL14-A
47UA
(Pp)
dipeptidepolymer2296.41Saccharomyces cerevisiae
48VA
(Q)
60S ribosomal protein L32polymer13014809.41UniProt (P38061)
Pfam (PF01655)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL32
49WA
(QQ)
60S ribosomal protein L15-Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)
Saccharomyces cerevisiae (baker's yeast)L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18
50XA
(R)
60S ribosomal protein L33-Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)
Saccharomyces cerevisiae (baker's yeast)L37,Large ribosomal subunit protein eL33-A,RP47,YL37
51YA
(S)
60S ribosomal protein L34-Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL34-A
52ZA
(T)
60S ribosomal protein L35-Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein uL29-A
53AB
(U)
60S ribosomal protein L36-Apolymer10011151.31UniProt (P05745)
Pfam (PF01158)
Saccharomyces cerevisiae (baker's yeast)L39,Large ribosomal subunit protein eL36-A,YL39
54BB
(V)
60S ribosomal protein L37-Apolymer889877.41UniProt (P49166)
Pfam (PF01907)
Saccharomyces cerevisiae (baker's yeast)L43,Large ribosomal subunit protein eL37-A,YL35,YP55
55CB
(W)
60S ribosomal protein L38polymer788845.61UniProt (P49167)
Pfam (PF01781)
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL38
56DB
(X)
60S ribosomal protein L39polymer516358.61UniProt (P04650)
Pfam (PF00832)
Saccharomyces cerevisiae (baker's yeast)L46,Large ribosomal subunit protein eL39,YL40
57EB
(Y)
Ubiquitin-60S ribosomal protein L40polymer12814583.11UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)
Saccharomyces cerevisiae (baker's yeast)
58FB
(Z)
60S ribosomal protein L41-Apolymer253354.21UniProt (P0CX86)
Pfam (PF05162)
Saccharomyces cerevisiae (baker's yeast)L47,Large ribosomal subunit protein eL41-A,YL41
59GB
(a)
60S ribosomal protein L42-Apolymer10612246.71UniProt (P0CX27)
Pfam (PF00935)
Saccharomyces cerevisiae (baker's yeast)L41,Large ribosomal subunit protein eL42-A,YL27,YP44
60HB
(b)
60S ribosomal protein L43-Apolymer9210113.01UniProt (P0CX25)
Pfam (PF01780)
Saccharomyces cerevisiae (baker's yeast)L37a,Large ribosomal subunit protein eL43-A,YL35
61IB
(c)
18S ribosomal RNApolymer1800580284.71Saccharomyces cerevisiae
62JB
(d)
40S ribosomal protein S0-Apolymer25228051.31UniProt (P32905)
Pfam (PF00318)
Saccharomyces cerevisiae (baker's yeast)Nucleic acid-binding protein NAB1A,Small ribosomal subunit protein uS2-A
63KB
(e)
40S ribosomal protein S1-Apolymer25528798.51UniProt (A7A1W1)
Pfam (PF01015)
UniProt (by SIFTS) (P33442)
Saccharomyces cerevisiae (baker's yeast)
64LB
(f)
40S ribosomal protein S2polymer25427490.81UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
Saccharomyces cerevisiae (baker's yeast)Omnipotent suppressor protein SUP44,RP12,S4,Small ribosomal subunit protein uS5,YS5
65MB
(g)
RPS3 isoform 1polymer24026542.81UniProt (A0A6A5Q3Q1)
Pfam (PF07650)
Pfam (PF00189)
UniProt (by SIFTS) (P05750)
Saccharomyces cerevisiae (baker's yeast)
66NB
(h)
40S ribosomal protein S4-Apolymer26129469.31UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
Saccharomyces cerevisiae (baker's yeast)RP5,S7,Small ribosomal subunit protein eS4-A,YS6
67OB
(i)
40S ribosomal protein S5polymer22525072.61UniProt (P26783)
Pfam (PF00177)
Saccharomyces cerevisiae (baker's yeast)RP14,S2,Small ribosomal subunit protein uS7,YS8
68PB
(j)
40S ribosomal protein S6-Apolymer23627054.51UniProt (P0CX37)
Pfam (PF01092)
Saccharomyces cerevisiae (baker's yeast)RP9,S10,Small ribosomal subunit protein eS6-A,YS4
69QB
(k)
40S ribosomal protein S7-Apolymer19021658.21UniProt (P26786)
Pfam (PF01251)
Saccharomyces cerevisiae (baker's yeast)RP30,RP40,Small ribosomal subunit protein eS7-A
70RB
(l)
40S ribosomal protein S8-Bpolymer20022537.81UniProt (P0CX40)
Pfam (PF01201)
Saccharomyces cerevisiae (baker's yeast)RP19,S14,Small ribosomal subunit protein eS8-B,YS9
71SB
(m)
40S ribosomal protein S9-Apolymer19722487.91UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
Saccharomyces cerevisiae (baker's yeast)RP21,S13,Small ribosomal subunit protein uS4-A,YP28,YS11
72TB
(n)
40S ribosomal protein S10-Apolymer10512757.41UniProt (Q08745)
Pfam (PF03501)
Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein eS10-A
73UB
(o)
40S ribosomal protein S11-Apolymer15617785.91UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
Saccharomyces cerevisiae (baker's yeast)RP41,S18,Small ribosomal subunit protein uS17-A,YS12
74VB
(p)
40S ribosomal protein S13polymer15117059.91UniProt (P05756)
Pfam (PF00312)
Pfam (PF08069)
Saccharomyces cerevisiae (baker's yeast)S27a,Small ribosomal subunit protein uS15,YS15
75WB
(q)
40S ribosomal protein S14-Apolymer13714562.71UniProt (P06367)
Pfam (PF00411)
Saccharomyces cerevisiae (baker's yeast)RP59A,Small ribosomal subunit protein uS11-A
76XB
(r)
40S ribosomal protein S15polymer14216031.91UniProt (Q01855)
Pfam (PF00203)
Saccharomyces cerevisiae (baker's yeast)RIG protein,RP52,S21,Small ribosomal subunit protein uS19,YS21
77YB
(s)
40S ribosomal protein S16-Apolymer14315877.51UniProt (P0CX51)
Pfam (PF00380)
Saccharomyces cerevisiae (baker's yeast)RP61R,Small ribosomal subunit protein uS9-A
78ZB
(t)
40S ribosomal protein S17-Apolymer13615820.41UniProt (P02407)
Pfam (PF00833)
Saccharomyces cerevisiae (baker's yeast)RP51A,Small ribosomal subunit protein eS17-A
79AC
(u)
40S ribosomal protein S18-Apolymer14617071.61UniProt (P0CX55)
Pfam (PF00416)
Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein uS13-A
80BC
(v)
40S ribosomal protein S19-Apolymer14415942.11UniProt (P07280)
Pfam (PF01090)
Saccharomyces cerevisiae (baker's yeast)RP55A,S16a,Small ribosomal subunit protein eS19-A,YP45,YS16A
81CC
(w)
40S ribosomal protein S20polymer12113929.01UniProt (A0A6A5PVE9)
Pfam (PF00338)
UniProt (by SIFTS) (P38701)
Saccharomyces cerevisiae (baker's yeast)BJ4_G0000330.mRNA.1.CDS.1,BJ4_G0023380.mRNA.1.CDS.1,EM14S01-3B_G0053970.mRNA.1.CDS.1,HLJ1_G0023150.mRNA.1.CDS.1,HLJ1_G0054920.mRNA.1.CDS.1,HN1_G0054660.mRNA.1.CDS.1,SX2_G0054700.mRNA.1.CDS.1,Y55_G0054930.mRNA.1.CDS.1
82DC
(x)
40S ribosomal protein S21-Apolymer879758.81UniProt (P0C0V8)
Pfam (PF01249)
Saccharomyces cerevisiae (baker's yeast)S26,Small ribosomal subunit protein eS21-A,YS25
83EC
(y)
40S ribosomal protein S22-Apolymer13014650.11UniProt (P0C0W1)
Pfam (PF00410)
Saccharomyces cerevisiae (baker's yeast)RP50,S24,Small ribosomal subunit protein uS8-A,YP58,YS22
84FC
(z)
40S ribosomal protein S23-Apolymer14516073.91UniProt (P0CX29)
Pfam (PF00164)
Saccharomyces cerevisiae (baker's yeast)RP37,S28,Small ribosomal subunit protein uS12-A,YS14
85GC, HC, IC, NL, OL...
(2, 5, 8, S, V...)
ZINC IONnon-polymer65.48Chemie (ZN)
86AD, AE, AF, AG, AH...
(AA, Bb, c, CC, FF...)
MAGNESIUM IONnon-polymer24.3267Chemie (MG)
87EE, FE, GE, WL
(AA, c)
SPERMIDINEnon-polymer145.24Chemie (SPD)
88BG, CG, DG, EG, EL...
(AA, CC, EE, MM, Q...)
POTASSIUM IONnon-polymer39.121Chemie (K)
89RK
(Aa)
GUANOSINE-5'-DIPHOSPHATEnon-polymer443.21Chemie (GDP)
90SK
(Aa)
[1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACIDnon-polymer494.61Chemie (SO1)
91AO, BO, CO, DO, EO...
(BB, CC, Cc, D, EE...)
waterwater18.01086Chemie (HOH)
Sequence modifications
Cc: 1 - 77 (GenBank: 170517292)
PDBExternal DatabaseDetails
C 18U 3030542conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains84
Total formula weight3299204.7
Non-Polymers*Number of molecules302
Total formula weight9352.6
All*Total formula weight3308557.3
*Water molecules are not included.

227111

PDB entries from 2024-11-06

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