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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6AZ3

Cryo-EM structure of of the large subunit of Leishmania ribosome bound to paromomycin

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1Aribosomal protein uL2polymer25427521.01Leishmania donovani
2Bribosomal protein uL3polymer40245741.41Leishmania donovani
3CRibosomal protein L1a, putativepolymer36640523.21UniProt (A0A3S5H7L0)
Pfam (PF00573)
Pfam (PF14374)
In PDB		Leishmania donovaniRibosomal protein L4/L1 family protein,Ribosomal_protein_L1a_putative/GeneDB:LmjF.29.107 0/GeneDB:LmjF.29.1090
4D60S ribosomal protein L11 (L5, L16)polymer16819245.31UniProt (A0A3S5H5A8)
Pfam (PF00281)
Pfam (PF00673)
In PDB		Leishmania donovani60S_ribosomal_protein_L11_(L5_L16)/GeneDB:LmjF.04.0470/GeneDB:LmjF.22.0030,ADP-ribosylation_factor_putative/GeneDB:LmjF.04.0 480,Ribosomal L5P C-terminus family protein
5E60S ribosomal protein L9, putativepolymer18621118.71UniProt (A0A3S7X3V0)
Pfam (PF00347)
In PDB		Leishmania donovani60S_ribosomal_protein_L9_putative/GeneDB:LmjF.21. 1050/GeneDB:LmjF.30.3340,Ribosomal protein L6 family protein
6Fribosomal protein eL6polymer19521208.91Leishmania donovani
7G60S ribosomal protein L7apolymer34839175.21UniProt (E9B949)
Pfam (PF01248)
In PDB		Leishmania donovani
8Hribosomal protein uL13polymer22125346.01Leishmania donovani
9Iribosomal protein eL13polymer21223897.91Leishmania donovani
10J60S ribosomal protein L23, putativepolymer13414422.01UniProt (A0A3Q8IIA7)
Pfam (PF00238)
In PDB		Leishmania donovani60S_ribosomal_protein_L23_putative/GeneDB:LmjF.35.3790/GeneDB:LmjF.35.3800,Ribosomal protein L14p/L23e family protein
11KProbable 60S ribosomal protein L14polymer14917039.01UniProt (Q25278)
Pfam (PF01929)
Pfam (PF00467)
In PDB		Leishmania donovani23 kDa cell surface protein,LDP 23
12L60S ribosomal protein L27A/L29, putativepolymer14416034.71UniProt (A0A3Q8IGI9)
Pfam (PF00828)
In PDB		Leishmania donovani60S_ribosomal_protein_L27A/L29_putative/GeneDB:Lm jF.35.3760/GeneDB:LmjF.35.3780,Ribosomal protein L18e/L15 family protein
13MRibosomal protein L15polymer20324366.81UniProt (A0A3Q8IIZ6)
Pfam (PF00827)
UniProt (by SIFTS) (E9BMB4)
In PDB		Leishmania donovani
14N60S ribosomal protein L10, putativepolymer21324607.21UniProt (A0A3S5H5C4)
Pfam (PF00252)
In PDB		Leishmania donovani60S_ribosomal_protein_L10_putative/GeneDB:LmjF.04.0750/GeneDB:LmjF.04.0950,Hypothetical_protein,Ribosomal protein L10.e
15O60S ribosomal protein L5, putativepolymer30534100.61UniProt (A0A3Q8IJC5)
Pfam (PF17144)
Pfam (PF14204)
In PDB		Leishmania donovani60S_ribosomal_protein_L5_putative/GeneDB:LmjF.35. 1880/GeneDB:LmjF.35.1890/GeneDB:LmjF.35.1900,Ribosomal L18p/L5e family protein
16P60S ribosomal protein L18, putativepolymer19721939.91UniProt (A0A3S7XBN1)
Pfam (PF17135)
In PDB		Leishmania donovani60S_ribosomal_protein_L18_putative/GeneDB:LmjF.13.0560/GeneDB:LmjF.36.4510,Ribosomal protein L18e/L15 family protein
17QRibosomal protein L19e family proteinpolymer18922901.01UniProt (A0A504XXD2)
Pfam (PF01280)
In PDB		Leishmania donovani
18R60S ribosomal protein L18apolymer17820703.21UniProt (A0A3Q8IT55)
Pfam (PF01775)
In PDB		Leishmania donovani
19S60S ribosomal protein L21, putativepolymer15417437.41UniProt (A0A3Q8ICH0)
Pfam (PF01157)
In PDB		Leishmania donovani60S_ribosomal_protein_L21_putative/GeneDB:LmjF.16.0460/GeneDB:LmjF.34.3650,Ribosomal protein L21e family protein
20T60S ribosomal protein L17, putativepolymer15417828.91UniProt (A0A3S7WY02)
Pfam (PF00237)
In PDB		Leishmania donovaniRibosomal protein L22,Ribosomal_protein_L22p/L17e_putative/Pfam:PF00237
21U60S ribosomal protein L22, putativepolymer12114042.51UniProt (A0A3Q8IJA8)
Pfam (PF01776)
In PDB		Leishmania donovani60S_ribosomal_protein_L22_putative/GeneDB:LmjF.36.3270/GeneDB:LmjF.36.4420,Ribosomal L22e family protein
22V60S ribosomal protein L23a, putativepolymer11813461.81UniProt (A0A3S7WPH7)
Pfam (PF00276)
UniProt (by SIFTS) (E9B8R9)
In PDB		Leishmania donovani60S_ribosomal_protein_L23a_putative/GeneDB:LmjF.0 6.0570/GeneDB:LmjF.06.0580,Archaeal ribosomal protein L23
23Wribosomal protein uL24polymer12113874.41Leishmania donovani
24Xribosomal protein eL24polymer657988.51Leishmania donovani
25YRibosomal L27e family proteinpolymer13215223.01UniProt (A0A504XEJ0)
Pfam (PF01777)
In PDB		Leishmania donovani
26Z60S ribosomal protein L28, putativepolymer14015525.91UniProt (A0A3Q8I959)
Pfam (PF01778)
In PDB		Leishmania donovani60S_ribosomal_protein_L28_putative/GeneDB:LmjF.11.1110/GeneDB:LmjF.11.1130,Ribosomal L28e family protein
27a60S_ribosomal_protein_L35_putative/GeneDB:LmjF.26.2330/GeneDB:LmjF.26.2340polymer12514987.81UniProt (A0A504XWA8)
Pfam (PF00831)
UniProt (by SIFTS) (E9BIP6)
In PDB		Leishmania donovaniRibosomal L29 family protein
28b60S ribosomal protein L29polymer687788.11UniProt (A0A504XJE6)
Pfam (PF01779)
In PDB		Leishmania donovani
29c60S ribosomal protein L7 family proteinpolymer22726313.11UniProt (A0A504XVT8)
Pfam (PF08079)
Pfam (PF00327)
In PDB		Leishmania donovani
30d60S ribosomal protein L30polymer9210122.71UniProt (A0A3Q8IET6)
Pfam (PF01248)
In PDB		Leishmania donovani60S_ribosomal_protein_L30/GeneDB:LmjF.35.0240,Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein
31e60S ribosomal subunit protein L31, putativepolymer11913503.01UniProt (A0A3Q8IJL7)
Pfam (PF01198)
In PDB		Leishmania donovani60S_ribosomal_subunit_protein_L31_putative/GeneDB:LmjF.35.3280/GeneDB:LmjF.35.3290,Ribosomal protein L31e family protein
32f60S_ribosomal_protein_L32/GeneDB:LmjF.21.1720polymer13015029.61UniProt (A0A504XZK6)
Pfam (PF01655)
In PDB		Leishmania donovaniRibosomal protein L32 family protein
33gRibosomal protein L35Ae family proteinpolymer12514336.81UniProt (A0A3Q8II82)
Pfam (PF01247)
In PDB		Leishmania donovaniRibosomal protein l35a,putative,Ribosomal_protein_l35a_putative/GeneDB:LmjF.10.00 70/GeneDB:LmjF.34.2470
34h60S ribosomal protein L34, putativepolymer12514640.31UniProt (A0A3Q8IHK2)
Pfam (PF01199)
In PDB		Leishmania donovani60S_ribosomal_protein_L34_putative/GeneDB:LmjF.18.1400
35i60S ribosomal protein L36, putativepolymer9711050.11UniProt (A0A3Q8IDW6)
Pfam (PF01158)
In PDB		Leishmania donovani60S_ribosomal_protein_L36_putative/GeneDB:LmjF.21.0730,Ribosomal protein L36e family protein
36j60S ribosomal protein L37polymer809531.11UniProt (P62885)
Pfam (PF01907)
In PDB		Leishmania donovani
37kRibosomal L38e family proteinpolymer768761.51UniProt (A0A504WZU0)
Pfam (PF01781)
In PDB		Leishmania donovani
38l60S ribosomal protein L39, putativepolymer506373.61UniProt (A0A3Q8IAG7)
Pfam (PF00832)
UniProt (by SIFTS) (E9BCX6)
In PDB		Leishmania donovani60S_ribosomal_protein_L39_putative/GeneDB:LmjF.16.1170/GeneDB:LmjF.29.2370
39mUbiquitin-60S ribosomal protein L40polymer505912.31UniProt (A0A3Q8ISR1)
Pfam (PF01020)
In PDB		Leishmania donovani
40nribosomal protein eL41polymer334259.31Leishmania donovani
41o60S ribosomal protein L37apolymer9010092.91UniProt (A0A3Q8IC65)
Pfam (PF01780)
UniProt (by SIFTS) (E9BFK4)
In PDB		Leishmania donovani60S_ribosomal_protein_L37a/GeneDB:LmjF.36.1925
42p60S ribosomal protein L44, putativepolymer9611141.41UniProt (A0A3Q8IKJ4)
Pfam (PF00935)
UniProt (by SIFTS) (E9BBL5)
In PDB		Leishmania donovani60S_ribosomal_protein_L44_putative/GeneDB:LmjF.13.1670,Ribosomal protein L44 family protein
431rRNA alphapolymer1778575707.61GenBank (322500086)Leishmania donovani
442rRNA betapolymer1526492460.81GenBank (322500086)Leishmania donovani
453rRNA gammapolymer21167568.81GenBank (322500086)Leishmania donovani
464rRNA deltapolymer18359144.11GenBank (5019758)Leishmania donovani
475rRNA epsilonpolymer13342869.41GenBank (5019758)Leishmania donovani
486rRNA zetapolymer7122725.61GenBank (5019758)Leishmania donovani
497rRNA 5.8Spolymer17154989.61GenBank (1229082208)Leishmania donovani
508rRNA 5Spolymer11837923.51GenBank (1229082190)Leishmania donovani
511, 2, 7PAROMOMYCINnon-polymer615.610Chemie (PAR)
521, 2, 3, 4, 5...MAGNESIUM IONnon-polymer24.334Chemie (MG)
53waterwater18.01019Chemie (HOH)
Sequence modifications
V: 28 - 144 (UniProt: A0A3S7WPH7)
PDBExternal DatabaseDetails
Ala 27-expression tag
1: 3 - 1782 (GenBank: 322500086)
PDBExternal DatabaseDetails
-A 1017649deletion
-A 1017504deletion
3: 2 - 213 (GenBank: 322500086)
PDBExternal DatabaseDetails
-U 1017041deletion
C 196A 1016865conflict
8: 3 - 120 (GenBank: 1229082190)
PDBExternal DatabaseDetails
U 14C 281956conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains50
Total formula weight2112507.3
Non-Polymers*Number of molecules44
Total formula weight6982.7
All*Total formula weight2119489.9
*Water molecules are not included.

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PDB entries from 2024-07-10

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