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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5DGF

Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
12, 618S ribosomal RNApolymer1800579761.92GenBank (874346701)Saccharomyces cerevisiae S288c
2S0, s040S ribosomal protein S0-Apolymer25127920.12UniProt (P32905)
Pfam (PF00318)
In PDB		Saccharomyces cerevisiae S288cNucleic acid-binding protein NAB1A
3S1, s140S ribosomal protein S1-Apolymer25428667.32UniProt (P33442)
Pfam (PF01015)
In PDB		Saccharomyces cerevisiae S288cRP10A
4S2, s240S ribosomal protein S2polymer25327359.62UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
In PDB		Saccharomyces cerevisiae S288cOmnipotent suppressor protein SUP44,RP12,S4,YS5
5S3, s340S ribosomal protein S3polymer23926411.62UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
In PDB		Saccharomyces cerevisiae S288cRP13,YS3
6S4, s440S ribosomal protein S4-Apolymer26029338.12UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
In PDB		Saccharomyces cerevisiae S288cRP5,S7,YS6
7S5, s540S ribosomal protein S5polymer22424941.42UniProt (P26783)
Pfam (PF00177)
In PDB		Saccharomyces cerevisiae S288cRP14,S2,YS8
8S6, s640S ribosomal protein S6-Apolymer23627054.52UniProt (P0CX37)
Pfam (PF01092)
In PDB		Saccharomyces cerevisiae S288cRP9,S10,YS4
9S7, s740S ribosomal protein S7-Apolymer18921527.02UniProt (P26786)
Pfam (PF01251)
In PDB		Saccharomyces cerevisiae S288cRP30,RP40
10S8, s840S ribosomal protein S8-Apolymer20022537.82UniProt (P0CX39)
Pfam (PF01201)
In PDB		Saccharomyces cerevisiae S288cRP19,S14,YS9
11S9, s940S ribosomal protein S9-Apolymer19622356.72UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
In PDB		Saccharomyces cerevisiae S288cRP21,S13,YP28,YS11
12C0, c040S ribosomal protein S10-Apolymer9611137.82Saccharomyces cerevisiae S288c
13C1, c140S ribosomal protein S11-Apolymer15517396.52Saccharomyces cerevisiae S288cRP41,S18,YS12
14C2, c240S ribosomal protein S12polymer14214976.12Saccharomyces cerevisiae S288c
15C3, c340S ribosomal protein S13polymer15016928.72UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
In PDB		Saccharomyces cerevisiae S288cS27a,YS15
16C4, c440S ribosomal protein S14-Apolymer13614431.52UniProt (P06367)
Pfam (PF00411)
In PDB		Saccharomyces cerevisiae S288cRP59A
17C5, c540S ribosomal protein S15 (uS19)polymer14115797.62Saccharomyces cerevisiae S288c
18C6, c640S ribosomal protein S16-Apolymer14215746.32UniProt (P0CX51)
Pfam (PF00380)
In PDB		Saccharomyces cerevisiae S288cRP61R
19C7, c740S ribosomal protein S17-Apolymer13615820.42UniProt (P02407)
Pfam (PF00833)
In PDB		Saccharomyces cerevisiae S288cRP51A
20C8, c840S ribosomal protein S18-Apolymer14516940.42UniProt (P0CX55)
Pfam (PF00416)
In PDB		Saccharomyces cerevisiae S288c
21C9, c940S ribosomal protein S19-Apolymer14315810.92UniProt (P07280)
Pfam (PF01090)
In PDB		Saccharomyces cerevisiae S288cRP55A,S16a,YP45,YS16A
22D0, d040S ribosomal protein S20polymer12013797.92UniProt (P38701)
Pfam (PF00338)
In PDB		Saccharomyces cerevisiae S288c
23D1, d140S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)
In PDB		Saccharomyces cerevisiae S288cS26,YS25
24D2, d240S ribosomal protein S22-Apolymer12914518.92UniProt (P0C0W1)
Pfam (PF00410)
In PDB		Saccharomyces cerevisiae S288cRP50,S24,YP58,YS22
25D3, d340S ribosomal protein S23-Apolymer14415942.72UniProt (P0CX29)
Pfam (PF00164)
In PDB		Saccharomyces cerevisiae S288cRP37,S28,YS14
26D4, d440S ribosomal protein S24-Apolymer13415231.62UniProt (P0CX31)
Pfam (PF01282)
In PDB		Saccharomyces cerevisiae S288cRP50
27D5, d540S ribosomal protein S25-Apolymer10711936.12UniProt (Q3E792)
Pfam (PF03297)
In PDB		Saccharomyces cerevisiae S288cRP45,S31,YS23
28D6, d640S ribosomal protein S26-Bpolymer9711023.02UniProt (P39939)
Pfam (PF01283)
In PDB		Saccharomyces cerevisiae S288c
29D7, d740S ribosomal protein S27-Apolymer818762.22UniProt (P35997)
Pfam (PF01667)
In PDB		Saccharomyces cerevisiae S288cRP61,YS20
30D8, d840S ribosomal protein S28-Apolymer667474.72UniProt (Q3E7X9)
Pfam (PF01200)
In PDB		Saccharomyces cerevisiae S288cS33,YS27
31D9, d940S ribosomal protein S29-Apolymer556544.52UniProt (P41057)
Pfam (PF00253)
In PDB		Saccharomyces cerevisiae S288cS36,YS29
32E0, e040S ribosomal protein S30-Apolymer627006.32UniProt (P0CX33)
Pfam (PF04758)
In PDB		Saccharomyces cerevisiae S288c
33E1, e1Ubiquitin-40S ribosomal protein S31polymer768703.52UniProt (P05759)
Pfam (PF01599)
In PDB		Saccharomyces cerevisiae S288c
34SR, sRGuanine nucleotide-binding protein subunit beta-like proteinpolymer31834710.02UniProt (P38011)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae S288cReceptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
35SM, sMSuppressor protein STM1polymer27328715.12Saccharomyces cerevisiae S288c3BP1,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
361, 525S ribosomal RNApolymer33961097493.92GenBank (831416132)Saccharomyces cerevisiae S288c
373, 75S ribosomal RNApolymer12138951.12GenBank (834774822)Saccharomyces cerevisiae S288c
384, 85.8S ribosomal RNApolymer15850682.92GenBank (941508018)Saccharomyces cerevisiae S288c
39L2, l260S ribosomal protein L2-Apolymer25327332.42UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
In PDB		Saccharomyces cerevisiae S288cL5,RP8,YL6
40L3, l360S ribosomal protein L3polymer38643719.62UniProt (P14126)
Pfam (PF00297)
In PDB		Saccharomyces cerevisiae S288cMaintenance 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 S288cL2,RP2,YL2
42L5, l560S ribosomal protein L5polymer29633633.62UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
In PDB		Saccharomyces cerevisiae S288cL1,L1a,Ribosomal 5S RNA-binding protein,YL3
43L6, l660S ribosomal protein L6-Apolymer17519869.42UniProt (Q02326)
Pfam (PF01159)
In PDB		Saccharomyces cerevisiae S288cL17,RP18,YL16
44L7, l760S ribosomal protein L7-Apolymer24327555.12UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
In PDB		Saccharomyces cerevisiae S288cL6,RP11,YL8
45L8, l860S ribosomal protein L8-Apolymer25528058.62UniProt (P17076)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae S288cL4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
46L9, l960S ribosomal protein L9-Apolymer19121605.12UniProt (P05738)
Pfam (PF00347)
In PDB		Saccharomyces cerevisiae S288cL8,RP24,YL11
47M0, m060S ribosomal protein L10polymer22025279.32UniProt (P41805)
Pfam (PF00252)
In PDB		Saccharomyces cerevisiae S288cL9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
48M1, m160S ribosomal protein L11-Bpolymer17319654.52UniProt (Q3E757)
Pfam (PF00281)
Pfam (PF00673)
In PDB		Saccharomyces cerevisiae S288cL16,RP39,YL22
49M3, m360S ribosomal protein L13-Apolymer19822473.02UniProt (Q12690)
Pfam (PF01294)
In PDB		Saccharomyces cerevisiae S288c
50M4, m460S ribosomal protein L14-Apolymer13715063.92UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
In PDB		Saccharomyces cerevisiae S288c
51M5, m560S ribosomal protein L15-Apolymer20324351.22UniProt (P05748)
Pfam (PF00827)
In PDB		Saccharomyces cerevisiae S288cL13,RP15R,YL10,YP18
52M6, m660S ribosomal protein L16-Apolymer19822116.02UniProt (P26784)
Pfam (PF00572)
In PDB		Saccharomyces cerevisiae S288cL13a,L21,RP22,YL15
53M7, m760S ribosomal protein L17-Apolymer18320458.32UniProt (P05740)
Pfam (PF00237)
In PDB		Saccharomyces cerevisiae S288cL20A,YL17
54M8, m860S ribosomal protein L18-Apolymer18520478.12UniProt (P0CX49)
Pfam (PF17135)
In PDB		Saccharomyces cerevisiae S288cRP28
55M9, m960S ribosomal protein L19-Apolymer18821631.12UniProt (P0CX82)
Pfam (PF01280)
In PDB		Saccharomyces cerevisiae S288cL23,RP15L,RP33,YL14
56N0, n060S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)
In PDB		Saccharomyces cerevisiae S288cL18a
57N1, n160S ribosomal protein L21-Apolymer15918148.12UniProt (Q02753)
Pfam (PF01157)
In PDB		Saccharomyces cerevisiae S288c
58N2, n260S ribosomal protein L22-Apolymer12013580.22UniProt (P05749)
Pfam (PF01776)
In PDB		Saccharomyces cerevisiae S288cL1c,RP4,YL31
59N3, n360S ribosomal protein L23-Apolymer13614362.82UniProt (P0CX41)
Pfam (PF00238)
In PDB		Saccharomyces cerevisiae S288cL17a,YL32
60N4, n460S ribosomal protein L24-Apolymer15517661.72UniProt (P04449)
Pfam (PF01246)
In PDB		Saccharomyces cerevisiae S288cL30,RP29,YL21
61N5, n560S ribosomal protein L25polymer14115656.42UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
In PDB		Saccharomyces cerevisiae S288cRP16L,YL25,YP42'
62N6, n660S ribosomal protein L26-Apolymer12614134.62UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
In PDB		Saccharomyces cerevisiae S288cL33,YL33
63N7, n760S ribosomal protein L27-Apolymer13515437.22UniProt (P0C2H6)
Pfam (PF01777)
In PDB		Saccharomyces cerevisiae S288c
64N8, n860S ribosomal protein L28polymer14816630.52UniProt (P02406)
Pfam (PF00828)
In PDB		Saccharomyces cerevisiae S288cL27a,L29,RP44,RP62,YL24
65N9, n960S ribosomal protein L29polymer586560.72UniProt (P05747)
Pfam (PF01779)
In PDB		Saccharomyces cerevisiae S288cYL43
66O0, o060S ribosomal protein L30polymer10411299.22UniProt (P14120)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae S288cL32,RP73,YL38
67O1, o160S ribosomal protein L31-Apolymer11212849.02UniProt (P0C2H8)
Pfam (PF01198)
In PDB		Saccharomyces cerevisiae S288cL34,YL28
68O2, o260S ribosomal protein L32polymer12914678.22UniProt (P38061)
Pfam (PF01655)
In PDB		Saccharomyces cerevisiae S288c
69O3, o360S ribosomal protein L33-Apolymer10612045.92UniProt (P05744)
Pfam (PF01247)
In PDB		Saccharomyces cerevisiae S288cL37,RP47,YL37
70O4, o460S ribosomal protein L34-Apolymer12013542.02UniProt (P87262)
Pfam (PF01199)
In PDB		Saccharomyces cerevisiae S288c
71O5, o560S ribosomal protein L35-Apolymer11913811.42UniProt (P0CX84)
Pfam (PF00831)
In PDB		Saccharomyces cerevisiae S288c
72O6, o660S ribosomal protein L36-Apolymer9911020.12UniProt (P05745)
Pfam (PF01158)
In PDB		Saccharomyces cerevisiae S288cL39,YL39
73O7, o760S ribosomal protein L37-Apolymer879746.22UniProt (P49166)
Pfam (PF01907)
In PDB		Saccharomyces cerevisiae S288cL43,YL35,YP55
74O8, o860S ribosomal protein L38polymer778714.42UniProt (P49167)
Pfam (PF01781)
In PDB		Saccharomyces cerevisiae S288c
75O9, o960S ribosomal protein L39polymer506227.42UniProt (P04650)
Pfam (PF00832)
In PDB		Saccharomyces cerevisiae S288cL46,YL40
76Q0, q0Ubiquitin-60S ribosomal protein L40polymer526032.32UniProt (P0CH08)
Pfam (PF01020)
In PDB		Saccharomyces cerevisiae S288c
77Q1, q160S ribosomal protein L41-Apolymer253354.22UniProt (P0CX86)
Pfam (PF05162)
In PDB		Saccharomyces cerevisiae S288cL47,YL41
78Q2, q260S ribosomal protein L42-Apolymer10512115.52UniProt (P0CX27)
Pfam (PF00935)
In PDB		Saccharomyces cerevisiae S288cL41,YL27,YP44
79Q3, q360S ribosomal protein L43-Apolymer919981.82UniProt (P0CX25)
Pfam (PF01780)
In PDB		Saccharomyces cerevisiae S288cL37a,YL35
80m260S ribosomal protein L12-A (uL11)polymer16514060.31Saccharomyces cerevisiae S288c
81p060S acidic ribosomal protein P0polymer31133158.71Saccharomyces cerevisiae S288cA0,L10E
82p1, p260S ribosomal protein P1 alpha/P2 betapolymer474017.92Saccharomyces cerevisiae S288c
83fEukaryotic translation initiation factor 5A-1polymer15717136.31UniProt (P23301)
Pfam (PF21485)
Pfam (PF01287)
In PDB		Saccharomyces cerevisiae S288ceIF-5A-1,Hypusine-containing protein HP2,eIF-4D
84B, CCH-CH-8AN-PRO-PROpolymer51152.82Saccharomyces cerevisiae S288c
85e1, o7, q0, D6, q2...ZINC IONnon-polymer65.416Chemie (ZN)
861, BSPARSOMYCINnon-polymer361.42Chemie (SPS)
875, f, 1, B, CMAGNESIUM IONnon-polymer24.312Chemie (MG)
885, 1osmium (III) hexamminenon-polymer286.43Chemie (OHX)
89waterwater18.012Chemie (HOH)
Sequence modifications
L8, l8: 2 - 256 (UniProt: P17076)
PDBExternal DatabaseDetails
Ala 119Gly 119conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains165
Total formula weight6283678.9
Non-Polymers*Number of molecules33
Total formula weight2920.2
All*Total formula weight6286599.1
*Water molecules are not included.

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PDB entries from 2024-04-17

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