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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9YPY

Ribosome with accommodated A-site tRNA, Structure V

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(5)		28S ribosomal RNApolymer36011166972.31GenBank (5LZS_5)Oryctolagus cuniculus (rabbit)
2B
(7)		5S ribosomal RNApolymer12038691.91GenBank (X06789.1)Oryctolagus cuniculus (rabbit)
3C
(8)		5.8S ribosomal RNApolymer15650143.61GenBank (2795784436)Oryctolagus cuniculus (rabbit)
4D
(9)		18S ribosomal RNApolymer1869602776.91GenBank (5LZS_9)Oryctolagus cuniculus (rabbit)
5E
(A)		Ribosomal protein L8polymer25728088.91UniProt (G1TT27)
Pfam (PF00181)
Pfam (PF03947)		Oryctolagus cuniculus (rabbit)
6F
(B)		Ribosomal protein L3polymer40346108.01UniProt (G1TL06)
Pfam (PF00297)		Oryctolagus cuniculus (rabbit)
7G
(C)		60S ribosomal protein L4polymer42547727.61UniProt (G1SVW5)
Pfam (PF00573)
Pfam (PF14374)		Oryctolagus cuniculus (rabbit)
8H
(D)		Large ribosomal subunit protein uL18polymer29734481.81UniProt (P19949)Oryctolagus cuniculus (rabbit)60S ribosomal protein L5
9I
(E)		60S ribosomal protein L6polymer29133028.31UniProt (G1SKF7)
Pfam (PF03868)
Pfam (PF01159)		Oryctolagus cuniculus (rabbit)
10J
(G)		60S ribosomal protein L7apolymer31936221.51UniProt (G1STW0)
Pfam (PF01248)		Oryctolagus cuniculus (rabbit)
11K
(H)		60S ribosomal protein L9polymer19221871.41UniProt (G1SWI6)
Pfam (PF00347)		Oryctolagus cuniculus (rabbit)
12L
(I)		60S ribosomal protein L10polymer21424643.11UniProt (B7NZQ2)
Pfam (PF00252)		Oryctolagus cuniculus (rabbit)Ribosomal protein L10 (Predicted)
13M
(J)		Ribosomal protein L11polymer17820288.51UniProt (G1TUB8)
Pfam (PF00281)
Pfam (PF00673)		Oryctolagus cuniculus (rabbit)
14N
(K)		60S ribosomal protein L7polymer24729201.81UniProt (G1TUB1)
Pfam (PF08079)
Pfam (PF00327)		Oryctolagus cuniculus (rabbit)
15O
(L)		60S ribosomal protein L13polymer21124331.71UniProt (G1TPV0)Oryctolagus cuniculus (rabbit)
16P
(M)		60S ribosomal protein L14polymer21823870.51UniProt (G1SZ12)
Pfam (PF01929)		Oryctolagus cuniculus (rabbit)
17Q
(N)		Ribosomal protein L15polymer20424207.31UniProt (G1T0C1)
Pfam (PF00827)		Oryctolagus cuniculus (rabbit)
18R
(O)		Large ribosomal subunit protein uL13polymer20323533.31UniProt (G1TVS8)Oryctolagus cuniculus (rabbit)60S ribosomal protein L13a
19S
(P)		Large ribosomal subunit protein uL22polymer18421444.21UniProt (G1SCJ6)
Pfam (PF00237)		Oryctolagus cuniculus (rabbit)60S ribosomal protein L17
20T
(Q)		Ribosomal protein L18polymer18821699.71UniProt (G1TFE0)
Pfam (PF17135)		Oryctolagus cuniculus (rabbit)
21U
(R)		Ribosomal protein L19polymer19623535.31UniProt (G1TJR3)
Pfam (PF01280)		Oryctolagus cuniculus (rabbit)
22V
(S)		60S ribosomal protein L18apolymer17620827.61UniProt (G1TTY7)
Pfam (PF01775)		Oryctolagus cuniculus (rabbit)
23W
(T)		eL21polymer16018610.01UniProt (G1SHQ2)
Pfam (PF01157)		Oryctolagus cuniculus (rabbit)
24X
(U)		eL22polymer12814813.01UniProt (G1TSG1)
Pfam (PF01776)		Oryctolagus cuniculus (rabbit)
25Y
(V)		Ribosomal protein L23polymer14014892.51UniProt (G1T6D1)
Pfam (PF00238)		Oryctolagus cuniculus (rabbit)
26Z
(W)		eL24polymer15717825.11UniProt (G1SE28)
Pfam (PF01246)		Oryctolagus cuniculus (rabbit)
27AA
(X)		eL23polymer15617768.21UniProt (G1SE76)
Pfam (PF03939)
Pfam (PF00276)		Oryctolagus cuniculus (rabbit)
28BA
(Y)		uL24polymer14517303.41UniProt (G1SQH0)
Pfam (PF16906)
Pfam (PF00467)		Oryctolagus cuniculus (rabbit)
29CA
(Z)		60S ribosomal protein L27polymer13615835.81UniProt (G1TXF6)
Pfam (PF00467)
Pfam (PF01777)		Oryctolagus cuniculus (rabbit)
30DA
(a)		60S ribosomal protein L27apolymer14816620.61UniProt (G1SNY0)
Pfam (PF00828)		Oryctolagus cuniculus (rabbit)
31EA
(b)		Large ribosomal subunit protein eL29polymer24526708.71UniProt (G1SGR6)
Pfam (PF01779)		Oryctolagus cuniculus (rabbit)60S ribosomal protein L29
32FA
(c)		eL30polymer11512807.11UniProt (G1TDL2)
Pfam (PF01248)		Oryctolagus cuniculus (rabbit)
33GA
(d)		eL31polymer12514494.91UniProt (G1SHG0)
Pfam (PF01198)		Oryctolagus cuniculus (rabbit)
34HA
(e)		Ribosomal protein L32polymer13515898.91UniProt (A0AAA9WVN6)Oryctolagus cuniculus (rabbit)
35IA
(f)		eL33polymer11012580.81UniProt (G1SF08)
Pfam (PF01247)		Oryctolagus cuniculus (rabbit)
36JA
(g)		Large ribosomal subunit protein eL34polymer11613196.91UniProt (G1TXG5)
Pfam (PF01199)		Oryctolagus cuniculus (rabbit)60S ribosomal protein L34
37KA
(h)		eL35polymer12314566.61UniProt (G1SIT5)
Pfam (PF00831)		Oryctolagus cuniculus (rabbit)
38LA
(i)		60S ribosomal protein L36polymer10512263.81UniProt (G1TTQ5)
Pfam (PF01158)		Oryctolagus cuniculus (rabbit)
39MA
(k)		eL38polymer708238.91UniProt (G1U3J0)
Pfam (PF01781)		Oryctolagus cuniculus (rabbit)
40NA
(l)		eL39polymer516455.81UniProt (G1TTN1)
Pfam (PF00832)		Oryctolagus cuniculus (rabbit)
41OA
(m)		Ubiquitin A-52 residue ribosomal protein fusion product 1polymer10211699.81UniProt (A0A2K5PSA0)
Pfam (PF00240)
Pfam (PF01020)		Oryctolagus cuniculus (rabbit)Ubiquitin-60S ribosomal protein L40
42PA
(n)		eL41polymer253473.51UniProt (A0A087WNH4)
Pfam (PF05162)		Oryctolagus cuniculus (rabbit)60s ribosomal protein l41
43QA
(o)		Large ribosomal subunit protein eL42polymer10612477.01UniProt (A0AAA9WX15)Oryctolagus cuniculus (rabbit)60S ribosomal protein L36a
44RA
(p)		eL43polymer9210299.41UniProt (G1SY53)
Pfam (PF01780)		Oryctolagus cuniculus (rabbit)
45SA
(r)		eL28polymer13715783.61UniProt (G1U7L1)
Pfam (PF01778)		Oryctolagus cuniculus (rabbit)
46TA
(AA)		uS2 (SA)polymer29532958.01UniProt (G1TLT8)
Pfam (PF00318)
Pfam (PF16122)		Oryctolagus cuniculus (rabbit)40S ribosomal protein SA, 37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40
47UA
(BB)		40S ribosomal protein S3apolymer26430002.11UniProt (G1SS70)
Pfam (PF01015)		Oryctolagus cuniculus (rabbit)
48VA
(CC)		Small ribosomal subunit protein uS5polymer29331327.41UniProt (O18789)
Pfam (PF00333)
Pfam (PF03719)		Oryctolagus cuniculus (rabbit)40S ribosomal protein S2
49WA
(DD)		Ribosomal protein S3polymer24326715.31UniProt (G1TNM3)
Pfam (PF07650)
Pfam (PF00189)		Oryctolagus cuniculus (rabbit)
50XA
(EE)		eS4 (S4 X isoform)polymer26329654.91UniProt (G1TK17)
Pfam (PF08071)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)		Oryctolagus cuniculus (rabbit)40S ribosomal protein S4
51YA
(FF)		Ribosomal protein S5polymer20422913.51UniProt (G1TFM5)
Pfam (PF00177)		Oryctolagus cuniculus (rabbit)
52ZA
(GG)		40S ribosomal protein S6polymer24928751.91UniProt (G1TM55)
Pfam (PF01092)		Oryctolagus cuniculus (rabbit)
53AB
(HH)		40S ribosomal protein S7polymer19422168.91UniProt (G1SVB0)Oryctolagus cuniculus (rabbit)
54BB
(II)		40S ribosomal protein S8polymer20824263.41UniProt (G1TJW1)
Pfam (PF01201)		Oryctolagus cuniculus (rabbit)
55CB
(JJ)		Ribosomal protein S9 (Predicted)polymer19422641.61UniProt (B7NZS8)
Pfam (PF00163)
Pfam (PF01479)		Oryctolagus cuniculus (rabbit)
56DB
(KK)		S10_plectin domain-containing proteinpolymer16518933.81UniProt (G1TPV3)
Pfam (PF03501)		Oryctolagus cuniculus (rabbit)
57EB
(LL)		Ribosomal protein S11polymer15818468.81UniProt (G1TRM4)
Pfam (PF16205)
Pfam (PF00366)		Oryctolagus cuniculus (rabbit)
58FB
(MM)		40S ribosomal protein S12polymer13214539.01UniProt (G1SFR8)
Pfam (PF01248)		Oryctolagus cuniculus (rabbit)
59GB
(NN)		Ribosomal protein S13polymer15117259.41UniProt (G1SP51)
Pfam (PF08069)
Pfam (PF00312)		Oryctolagus cuniculus (rabbit)
60HB
(OO)		Small ribosomal subunit protein uS11polymer16818134.01UniProt (A0AAA9WYR1)Oryctolagus cuniculus (rabbit)40S ribosomal protein S14
61IB
(PP)		uS19polymer14517049.21UniProt (G1U0Q2)
Pfam (PF00203)		Oryctolagus cuniculus (rabbit)
62JB
(QQ)		uS9polymer14616477.41UniProt (G1SGX4)
Pfam (PF00380)		Oryctolagus cuniculus (rabbit)
63KB
(RR)		eS17polymer13515552.11UniProt (G1TU13)
Pfam (PF00833)		Oryctolagus cuniculus (rabbit)
64LB
(SS)		uS13polymer15217759.81UniProt (G1TPG3)
Pfam (PF00416)		Oryctolagus cuniculus (rabbit)
65MB
(TT)		eS19polymer14516106.61UniProt (G1TN62)
Pfam (PF01090)		Oryctolagus cuniculus (rabbit)
66NB
(UU)		uS10polymer11913398.81UniProt (G1SIZ2)
Pfam (PF00338)		Oryctolagus cuniculus (rabbit)
67OB
(VV)		eS21polymer839124.41UniProt (G1TM82)
Pfam (PF01249)		Oryctolagus cuniculus (rabbit)40S ribosomal protein S21
68PB
(WW)		Ribosomal protein S15apolymer13014865.61UniProt (G1TG89)
Pfam (PF00410)		Oryctolagus cuniculus (rabbit)
69QB
(XX)		uS12polymer14315844.71UniProt (G1SZ47)
Pfam (PF00164)		Oryctolagus cuniculus (rabbit)40S ribosomal protein S23
70RB
(YY)		40S ribosomal protein S24polymer13015107.91UniProt (G1T3D8)
Pfam (PF01282)		Oryctolagus cuniculus (rabbit)
71SB
(ZZ)		eS25polymer12513776.21UniProt (G1TDB3)
Pfam (PF03297)		Oryctolagus cuniculus (rabbit)
72TB
(aa)		40S ribosomal protein S26polymer11513047.51UniProt (G1TFE8)
Pfam (PF01283)		Oryctolagus cuniculus (rabbit)
73UB
(bb)		40S ribosomal protein S27polymer849480.21UniProt (G1TZ76)
Pfam (PF01667)		Oryctolagus cuniculus (rabbit)
74VB
(cc)		Ribosomal protein S28polymer697855.11UniProt (G1TIB4)
Pfam (PF01200)		Oryctolagus cuniculus (rabbit)
75WB
(dd)		eS29polymer566690.81UniProt (G1U7M4)
Pfam (PF00253)		Oryctolagus cuniculus (rabbit)
76XB
(ee)		40S ribosomal protein S30polymer13314498.91UniProt (G1T8A2)
Pfam (PF00240)
Pfam (PF04758)		Oryctolagus cuniculus (rabbit)
77YB
(ff)		Ribosomal protein S27apolymer15618004.01UniProt (G1SK22)
Pfam (PF00240)
Pfam (PF01599)		Oryctolagus cuniculus (rabbit)
78ZB
(gg)		RACK1polymer31735115.71UniProt (G1SJB4)
Pfam (PF00400)		Oryctolagus cuniculus (rabbit)
79AC
(10)		MF mRNApolymer18559653.41Oryctolagus cuniculus
80BC
(12)		Phe-tRNApolymer7624478.51GenBank (176419)Saccharomyces cerevisiae
81CC, EC
(13, 11)		Met-tRNApolymer7524231.52GenBank (174924)Homo sapiens
82DC
(j)		Ribosomal protein L37polymer9711111.01UniProt (U3KPD5)
Pfam (PF01907)		Oryctolagus cuniculus (rabbit)
83FC
(5)		SPERMIDINEnon-polymer145.21Chemie (SPD)
84GC, HC, IC, JC, KC...
(g, m, o, p, dd...)		ZINC IONnon-polymer65.46Chemie (ZN)
85LC
(12)		GUANOSINE-5'-TRIPHOSPHATEnon-polymer523.21Chemie (GTP)
86MC
(12)		PHENYLALANINEnon-polymer165.21Chemie (PHE)
87NC, QC
(13, 11)		ADENOSINE-5'-TRIPHOSPHATEnon-polymer507.22Chemie (ATP)
88OC
(13)		METHIONINEnon-polymer149.21Chemie (MET)
Sequence modifications
5: 1 - 5069 (GenBank: 5LZS_5)
PDBExternal DatabaseDetails
C 1N 1conflict
C 3948-insertion
A 3949-insertion
U 3950-insertion
G 3951-insertion
A 3952-insertion
G 3953-insertion
A 3954-insertion
G 3955-insertion
G 3956-insertion
U 3957-insertion
G 3958-insertion
U 3959-insertion
A 3960-insertion
G 3961-insertion
A 3962-insertion
A 3963-insertion
U 3964-insertion
A 3965-insertion
A 3966-insertion
G 3967-insertion
U 3968-insertion
G 3969-insertion
G 3970-insertion
G 3971-insertion
A 3972-insertion
G 3973-insertion
G 3974-insertion
C 3975-insertion
C 3976-insertion
G 4035-insertion
G 4036-insertion
C 4037-insertion
C 4038-insertion
G 4039-insertion
C 4040-insertion
C 4041-insertion
G 4042-insertion
G 4043-insertion
U 4044-insertion
G 4045-insertion
A 4046-insertion
A 4047-insertion
A 4048-insertion
U 4049-insertion
A 4050-insertion
C 4051-insertion
C 4052-insertion
A 4053-insertion
C 4054-insertion
U 4055-insertion
A 4056-insertion
C 4057-insertion
U 4058-insertion
C 4059-insertion
U 4060-insertion
G 4061-insertion
A 4062-insertion
U 4063-insertion
7: 1 - 120 (GenBank: X06789.1)
PDBExternal DatabaseDetails
U 2N 2conflict
C 36N 36conflict
U 102N 102conflict
U 112N 112conflict
U 114N 114conflict
U 119C 119conflict
U 120N 120conflict
C: 1 - 425 (UniProt: G1SVW5)
PDBExternal DatabaseDetails
Lys 378-insertion
Val 379-insertion
Lys 380-insertion
Lys 381-insertion
Pro 382-insertion
Arg 383-insertion
Ala 384-insertion
Val 385-insertion
Gly 386-insertion
Ile 387-insertion
Lys 388-insertion
Gln 389-insertion
G: 1 - 319 (UniProt: G1STW0)
PDBExternal DatabaseDetails
Gly 244Cys 244conflict
K: 1 - 247 (UniProt: G1TUB1)
PDBExternal DatabaseDetails
Arg 61Gly 61conflict
Arg 93Gly 93conflict
Met 131Val 131conflict
Ile 153Val 153conflict
L: 1 - 211 (UniProt: G1TPV0)
PDBExternal DatabaseDetails
Ile 46-insertion
Ala 47-insertion
Pro 48-insertion
Arg 49-insertion
Pro 50-insertion
Ala 51-insertion
Ala 52-insertion
Gly 53-insertion
Pro 54-insertion
Q: 1 - 188 (UniProt: G1TFE0)
PDBExternal DatabaseDetails
Asp 4Asn 4conflict
Arg 14Trp 14conflict
Met 53Leu 53conflict
Arg 58Trp 58conflict
Arg 75Gln 75conflict
Ala 80Pro 80conflict
Val 86Ile 86conflict
Arg 104His 104conflict
Arg 110Cys 110conflict
Val 137Gly 137conflict
Gly 157Arg 157conflict
Arg 181Trp 181conflict
R: 1 - 196 (UniProt: G1TJR3)
PDBExternal DatabaseDetails
Arg 38Cys 38conflict
Arg 64Gln 64conflict
Thr 94Lys 94conflict
S: 1 - 175 (UniProt: G1TTY7)
PDBExternal DatabaseDetails
Met 1Thr 1conflict
Pro 18-insertion
Thr 19-insertion
Pro 20Ser 18conflict
Cys 22Ser 20conflict
Arg 23Pro 21conflict
Thr 24Ala 22conflict
Ser 49Leu 47conflict
Gln 50Glu 48conflict
Arg 95His 93conflict
Thr 101Ile 99conflict
Thr 102Met 100conflict
Gly 104Ser 102conflict
Ile 126Val 124conflict
Ile 132Met 130conflict
Ser 135Ala 133conflict
Lys 136Arg 134conflict
Arg 138Pro 136conflict
Lys 149Arg 147conflict
Lys 151Arg 149conflict
Thr 168Tyr 166conflict
Thr 169Ala 167conflict
Phe 176-insertion
U: 1 - 128 (UniProt: G1TSG1)
PDBExternal DatabaseDetails
Leu 18Val 18conflict
Gly 32Arg 32conflict
Ala 36Glu 36conflict
Phe 39Ser 39conflict
Gly 54Arg 54conflict
Val 60Ala 60conflict
Ser 62Thr 62conflict
Leu 63Ile 63conflict
Arg 97His 97conflict
Thr 106Ser 106conflict
Glu 126Asp 126conflict
k: 1 - 70 (UniProt: G1U3J0)
PDBExternal DatabaseDetails
Arg 3Gln 3conflict
Cys 38Tyr 38conflict
Thr 48Met 48conflict
Val 66Met 66conflict
m: 10 - 102 (UniProt: A0A2K5PSA0)
PDBExternal DatabaseDetails
Met 1-initiating methionine
Gly 2-expression tag
Asp 3-expression tag
Pro 4-expression tag
Glu 5-expression tag
Ser 6-expression tag
Gly 7-expression tag
Gly 8-expression tag
Cys 9-expression tag
AA: 1 - 295 (UniProt: G1TLT8)
PDBExternal DatabaseDetails
Thr 114Ala 114conflict
CC: 1 - 293 (UniProt: O18789)
PDBExternal DatabaseDetails
Asp 13Gly 13conflict
Ile 19Met 19conflict
EE: 1 - 263 (UniProt: G1TK17)
PDBExternal DatabaseDetails
Gly 25Ser 25conflict
Arg 51Lys 51conflict
Thr 78Ala 78conflict
Val 156Met 156conflict
II: 1 - 208 (UniProt: G1TJW1)
PDBExternal DatabaseDetails
Arg 47Gly 47conflict
TT: 1 - 145 (UniProt: G1TN62)
PDBExternal DatabaseDetails
Gly 119Trp 119conflict
VV: 1 - 83 (UniProt: G1TM82)
PDBExternal DatabaseDetails
Asn 3Ser 3conflict
Asp 4Asn 4conflict
Gln 33Pro 33conflict
Phe 50Ser 50conflict
Ala 75Ser 75conflict
Asp 76His 76conflict
Lys 81Gln 81conflict
aa: 1 - 115 (UniProt: G1TFE8)
PDBExternal DatabaseDetails
Arg 28Cys 28conflict
Ala 56Val 56conflict
Arg 109Pro 109conflict
12: 1 - 76 (GenBank: 176419)
PDBExternal DatabaseDetails
C 37G 37conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains83
Total formula weight3460502.2
Non-Polymers*Number of molecules12
Total formula weight2389.6
All*Total formula weight3462891.8
*Water molecules are not included.

246905

PDB entries from 2025-12-31

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