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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
1A
(A)		ribosomal protein uL2polymer25427521.01Leishmania donovani
2B
(B)		ribosomal protein uL3polymer40245741.41Leishmania donovani
3C
(C)		Ribosomal protein L1a, putativepolymer36640523.21UniProt (A0A3S5H7L0)
Pfam (PF00573)
Pfam (PF14374)		Leishmania donovaniRibosomal protein L4/L1 family protein,Ribosomal_protein_L1a_putative/GeneDB:LmjF.29.107 0/GeneDB:LmjF.29.1090
4D
(D)		60S ribosomal protein L11 (L5, L16)polymer16819245.31UniProt (A0A3S5H5A8)
Pfam (PF00281)
Pfam (PF00673)		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
5E
(E)		60S ribosomal protein L9, putativepolymer18621118.71UniProt (A0A3S7X3V0)
Pfam (PF00347)		Leishmania donovani60S_ribosomal_protein_L9_putative/GeneDB:LmjF.21. 1050/GeneDB:LmjF.30.3340,Ribosomal protein L6 family protein
6F
(F)		ribosomal protein eL6polymer19521208.91Leishmania donovani
7G
(G)		60S ribosomal protein L7apolymer34839175.21UniProt (E9B949)
Pfam (PF01248)		Leishmania donovani
8H
(H)		ribosomal protein uL13polymer22125346.01Leishmania donovani
9I
(I)		ribosomal protein eL13polymer21223897.91Leishmania donovani
10J
(J)		60S ribosomal protein L23, putativepolymer13414422.01UniProt (A0A3Q8IIA7)
Pfam (PF00238)		Leishmania donovani60S_ribosomal_protein_L23_putative/GeneDB:LmjF.35.3790/GeneDB:LmjF.35.3800,Ribosomal protein L14p/L23e family protein
11K
(K)		Probable 60S ribosomal protein L14polymer14917039.01UniProt (Q25278)
Pfam (PF01929)
Pfam (PF00467)		Leishmania donovani23 kDa cell surface protein,LDP 23
12L
(L)		60S ribosomal protein L27A/L29, putativepolymer14416034.71UniProt (A0A3Q8IGI9)
Pfam (PF00828)		Leishmania donovani60S_ribosomal_protein_L27A/L29_putative/GeneDB:Lm jF.35.3760/GeneDB:LmjF.35.3780,Ribosomal protein L18e/L15 family protein
13M
(M)		Ribosomal protein L15polymer20324366.81UniProt (A0A3Q8IIZ6)
Pfam (PF00827)
UniProt (by SIFTS) (E9BMB4)		Leishmania donovani
14N
(N)		60S ribosomal protein L10, putativepolymer21324607.21UniProt (A0A3S5H5C4)
Pfam (PF00252)		Leishmania donovani60S_ribosomal_protein_L10_putative/GeneDB:LmjF.04.0750/GeneDB:LmjF.04.0950,Hypothetical_protein,Ribosomal protein L10.e
15O
(O)		60S ribosomal protein L5, putativepolymer30534100.61UniProt (A0A3Q8IJC5)
Pfam (PF17144)
Pfam (PF14204)		Leishmania donovani60S_ribosomal_protein_L5_putative/GeneDB:LmjF.35. 1880/GeneDB:LmjF.35.1890/GeneDB:LmjF.35.1900,Ribosomal L18p/L5e family protein
16P
(P)		60S ribosomal protein L18, putativepolymer19721939.91UniProt (A0A3S7XBN1)
Pfam (PF17135)		Leishmania donovani60S_ribosomal_protein_L18_putative/GeneDB:LmjF.13.0560/GeneDB:LmjF.36.4510,Ribosomal protein L18e/L15 family protein
17Q
(Q)		Ribosomal protein L19e family proteinpolymer18922901.01UniProt (A0A504XXD2)
Pfam (PF01280)		Leishmania donovani
18R
(R)		60S ribosomal protein L18apolymer17820703.21UniProt (A0A3Q8IT55)
Pfam (PF01775)		Leishmania donovani
19S
(S)		60S ribosomal protein L21, putativepolymer15417437.41UniProt (A0A3Q8ICH0)
Pfam (PF01157)		Leishmania donovani60S_ribosomal_protein_L21_putative/GeneDB:LmjF.16.0460/GeneDB:LmjF.34.3650,Ribosomal protein L21e family protein
20T
(T)		60S ribosomal protein L17, putativepolymer15417828.91UniProt (A0A3S7WY02)
Pfam (PF00237)		Leishmania donovaniRibosomal protein L22,Ribosomal_protein_L22p/L17e_putative/Pfam:PF00237
21U
(U)		60S ribosomal protein L22, putativepolymer12114042.51UniProt (A0A3Q8IJA8)
Pfam (PF01776)		Leishmania donovani60S_ribosomal_protein_L22_putative/GeneDB:LmjF.36.3270/GeneDB:LmjF.36.4420,Ribosomal L22e family protein
22V
(V)		60S ribosomal protein L23a, putativepolymer11813461.81UniProt (A0A3S7WPH7)
Pfam (PF00276)
UniProt (by SIFTS) (E9B8R9)		Leishmania donovani60S_ribosomal_protein_L23a_putative/GeneDB:LmjF.0 6.0570/GeneDB:LmjF.06.0580,Archaeal ribosomal protein L23
23W
(W)		ribosomal protein uL24polymer12113874.41Leishmania donovani
24X
(X)		ribosomal protein eL24polymer657988.51Leishmania donovani
25Y
(Y)		Ribosomal L27e family proteinpolymer13215223.01UniProt (A0A504XEJ0)
Pfam (PF01777)		Leishmania donovani
26Z
(Z)		60S ribosomal protein L28, putativepolymer14015525.91UniProt (A0A3Q8I959)
Pfam (PF01778)		Leishmania donovani60S_ribosomal_protein_L28_putative/GeneDB:LmjF.11.1110/GeneDB:LmjF.11.1130,Ribosomal L28e family protein
27AA
(a)		60S_ribosomal_protein_L35_putative/GeneDB:LmjF.26.2330/GeneDB:LmjF.26.2340polymer12514987.81UniProt (A0A504XWA8)
Pfam (PF00831)
UniProt (by SIFTS) (E9BIP6)		Leishmania donovaniRibosomal L29 family protein
28BA
(b)		60S ribosomal protein L29polymer687788.11UniProt (A0A504XJE6)
Pfam (PF01779)		Leishmania donovani
29CA
(c)		60S ribosomal protein L7 family proteinpolymer22726313.11UniProt (A0A504XVT8)
Pfam (PF08079)
Pfam (PF00327)		Leishmania donovani
30DA
(d)		60S ribosomal protein L30polymer9210122.71UniProt (A0A3Q8IET6)
Pfam (PF01248)		Leishmania donovani60S_ribosomal_protein_L30/GeneDB:LmjF.35.0240,Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein
31EA
(e)		60S ribosomal subunit protein L31, putativepolymer11913503.01UniProt (A0A3Q8IJL7)
Pfam (PF01198)		Leishmania donovani60S_ribosomal_subunit_protein_L31_putative/GeneDB:LmjF.35.3280/GeneDB:LmjF.35.3290,Ribosomal protein L31e family protein
32FA
(f)		60S_ribosomal_protein_L32/GeneDB:LmjF.21.1720polymer13015029.61UniProt (A0A504XZK6)
Pfam (PF01655)		Leishmania donovaniRibosomal protein L32 family protein
33GA
(g)		Ribosomal protein L35Ae family proteinpolymer12514336.81UniProt (A0A3Q8II82)
Pfam (PF01247)		Leishmania donovaniRibosomal protein l35a,putative,Ribosomal_protein_l35a_putative/GeneDB:LmjF.10.00 70/GeneDB:LmjF.34.2470
34HA
(h)		60S ribosomal protein L34, putativepolymer12514640.31UniProt (A0A3Q8IHK2)
Pfam (PF01199)		Leishmania donovani60S_ribosomal_protein_L34_putative/GeneDB:LmjF.18.1400
35IA
(i)		60S ribosomal protein L36, putativepolymer9711050.11UniProt (A0A3Q8IDW6)
Pfam (PF01158)		Leishmania donovani60S_ribosomal_protein_L36_putative/GeneDB:LmjF.21.0730,Ribosomal protein L36e family protein
36JA
(j)		60S ribosomal protein L37polymer809531.11UniProt (P62885)
Pfam (PF01907)		Leishmania donovani
37KA
(k)		Ribosomal L38e family proteinpolymer768761.51UniProt (A0A504WZU0)
Pfam (PF01781)		Leishmania donovani
38LA
(l)		60S ribosomal protein L39, putativepolymer506373.61UniProt (A0A3Q8IAG7)
Pfam (PF00832)
UniProt (by SIFTS) (E9BCX6)		Leishmania donovani60S_ribosomal_protein_L39_putative/GeneDB:LmjF.16.1170/GeneDB:LmjF.29.2370
39MA
(m)		Ubiquitin-60S ribosomal protein L40polymer505912.31UniProt (A0A3Q8ISR1)
Pfam (PF01020)		Leishmania donovani
40NA
(n)		ribosomal protein eL41polymer334259.31Leishmania donovani
41OA
(o)		60S ribosomal protein L37apolymer9010092.91UniProt (A0A3Q8IC65)
Pfam (PF01780)
UniProt (by SIFTS) (E9BFK4)		Leishmania donovani60S_ribosomal_protein_L37a/GeneDB:LmjF.36.1925
42PA
(p)		60S ribosomal protein L44, putativepolymer9611141.41UniProt (A0A3Q8IKJ4)
Pfam (PF00935)
UniProt (by SIFTS) (E9BBL5)		Leishmania donovani60S_ribosomal_protein_L44_putative/GeneDB:LmjF.13.1670,Ribosomal protein L44 family protein
43QA
(1)		rRNA alphapolymer1778575707.61GenBank (322500086)Leishmania donovani
44RA
(2)		rRNA betapolymer1526492460.81GenBank (322500086)Leishmania donovani
45SA
(3)		rRNA gammapolymer21167568.81GenBank (322500086)Leishmania donovani
46TA
(4)		rRNA deltapolymer18359144.11GenBank (5019758)Leishmania donovani
47UA
(5)		rRNA epsilonpolymer13342869.41GenBank (5019758)Leishmania donovani
48VA
(6)		rRNA zetapolymer7122725.61GenBank (5019758)Leishmania donovani
49WA
(7)		rRNA 5.8Spolymer17154989.61GenBank (1229082208)Leishmania donovani
50XA
(8)		rRNA 5Spolymer11837923.51GenBank (1229082190)Leishmania donovani
51AB, AC, BB, BC, CB...
(1, 2, 7)		PAROMOMYCINnon-polymer615.610Chemie (PAR)
52DB, DC, EB, EC, FB...
(1, 2, 3, 4, 5...)		MAGNESIUM IONnon-polymer24.334Chemie (MG)
53AD, BD, CD, DD, ED...
(Q, R, S, T, V...)		waterwater18.01019Chemie (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.

246905

PDB entries from 2025-12-31

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