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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

4U4U

Crystal structure of Lycorine bound to the yeast 80S ribosome

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A, BC
(2, 6)		18S ribosomal RNApolymer1800579761.92GenBank (1262303)Saccharomyces cerevisiae ATCC 204508 / S288cRNA (1750-MER)
2B, CC
(S0, s0)		40S ribosomal protein S0-Apolymer25127920.12UniProt (P32905)
Pfam (PF00318)		Saccharomyces cerevisiae ATCC 204508 / S288cNucleic acid-binding protein NAB1A
3C, DC
(S1, s1)		40S ribosomal protein S1-Apolymer25428667.32UniProt (P33442)
Pfam (PF01015)		Saccharomyces cerevisiae ATCC 204508 / S288cRP10A
4D, EC
(S2, s2)		40S ribosomal protein S2polymer25327359.62UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)		Saccharomyces cerevisiae ATCC 204508 / S288cOmnipotent suppressor protein SUP44,RP12,S4,YS5
5E, FC
(S3, s3)		40S ribosomal protein S3polymer23926411.62UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)		Saccharomyces cerevisiae ATCC 204508 / S288cRP13,YS3
6F, GC
(S4, s4)		40S ribosomal protein S4-Apolymer26029338.12UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)		Saccharomyces cerevisiae ATCC 204508 / S288cRP5,S7,YS6
7G, HC
(S5, s5)		40S ribosomal protein S5polymer22424941.42UniProt (P26783)
Pfam (PF00177)		Saccharomyces cerevisiae ATCC 204508 / S288cRP14,S2,YS8
8H, IC
(S6, s6)		40S ribosomal protein S6-Apolymer23627054.52UniProt (P0CX37)
Pfam (PF01092)		Saccharomyces cerevisiae ATCC 204508 / S288cRP9,S10,YS4
9I, JC
(S7, s7)		40S ribosomal protein S7-Apolymer18921527.02UniProt (P26786)
Pfam (PF01251)		Saccharomyces cerevisiae ATCC 204508 / S288cRP30,RP40
10J, KC
(S8, s8)		40S ribosomal protein S8-Apolymer20022537.82UniProt (P0CX39)
Pfam (PF01201)		Saccharomyces cerevisiae ATCC 204508 / S288cRP19,S14,YS9
11K, LC
(S9, s9)		40S ribosomal protein S9-Apolymer19622356.72UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)		Saccharomyces cerevisiae ATCC 204508 / S288cRP21,S13,YP28,YS11
12L, MC
(C0, c0)		40S ribosomal protein S10-Apolymer10512771.52UniProt (Q08745)
Pfam (PF03501)		Saccharomyces cerevisiae ATCC 204508 / S288c
13M, NC
(C1, c1)		40S ribosomal protein S11-Apolymer15517668.82UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)		Saccharomyces cerevisiae ATCC 204508 / S288cRP41,S18,YS12
14N, OC
(C2, c2)		40S ribosomal protein S12polymer14215385.52UniProt (P48589)
Pfam (PF01248)		Saccharomyces cerevisiae ATCC 204508 / S288c
15O, PC
(C3, c3)		40S ribosomal protein S13polymer15016928.72UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)		Saccharomyces cerevisiae ATCC 204508 / S288cS27a,YS15
16P, QC
(C4, c4)		40S ribosomal protein S14-Apolymer13614431.52UniProt (P06367)
Pfam (PF00411)		Saccharomyces cerevisiae ATCC 204508 / S288cRP59A
17Q, RC
(C5, c5)		40S ribosomal protein S15polymer14115900.72UniProt (Q01855)
Pfam (PF00203)		Saccharomyces cerevisiae ATCC 204508 / S288cRIG protein,RP52,S21,YS21
18R, SC
(C6, c6)		40S ribosomal protein S16-Apolymer14215746.32UniProt (P0CX51)
Pfam (PF00380)		Saccharomyces cerevisiae ATCC 204508 / S288cRP61R
19S, TC
(C7, c7)		40S ribosomal protein S17-Apolymer13615820.42UniProt (P02407)
Pfam (PF00833)		Saccharomyces cerevisiae ATCC 204508 / S288cRP51A
20T, UC
(C8, c8)		40S ribosomal protein S18-Apolymer14516940.42UniProt (P0CX55)
Pfam (PF00416)		Saccharomyces cerevisiae ATCC 204508 / S288c
21U, VC
(C9, c9)		40S ribosomal protein S19-Apolymer14315810.92UniProt (P07280)
Pfam (PF01090)		Saccharomyces cerevisiae ATCC 204508 / S288cRP55A,S16a,YP45,YS16A
22V, WC
(D0, d0)		40S ribosomal protein S20polymer12013797.92UniProt (P38701)
Pfam (PF00338)		Saccharomyces cerevisiae ATCC 204508 / S288c
23W, XC
(D1, d1)		40S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)		Saccharomyces cerevisiae ATCC 204508 / S288cS26,YS25
24X, YC
(D2, d2)		40S ribosomal protein S22-Apolymer12914518.92UniProt (P0C0W1)
Pfam (PF00410)		Saccharomyces cerevisiae ATCC 204508 / S288cRP50,S24,YP58,YS22
25Y, ZC
(D3, d3)		40S ribosomal protein S23-Apolymer14415942.72UniProt (P0CX29)
Pfam (PF00164)		Saccharomyces cerevisiae ATCC 204508 / S288cRP37,S28,YS14
26AD, Z
(D4, d4)		40S ribosomal protein S24-Apolymer13415231.62UniProt (P0CX31)
Pfam (PF01282)		Saccharomyces cerevisiae ATCC 204508 / S288cRP50
27AA, BD
(D5, d5)		40S ribosomal protein S25-Apolymer10711936.12UniProt (Q3E792)
Pfam (PF03297)		Saccharomyces cerevisiae ATCC 204508 / S288cRP45,S31,YS23
28BA, CD
(D6, d6)		40S ribosomal protein S26-Bpolymer9711023.02UniProt (P39939)
Pfam (PF01283)		Saccharomyces cerevisiae ATCC 204508 / S288c
29CA, DD
(D7, d7)		40S ribosomal protein S27-Apolymer818762.22UniProt (P35997)
Pfam (PF01667)		Saccharomyces cerevisiae ATCC 204508 / S288cRP61,YS20
30DA, ED
(D8, d8)		40S ribosomal protein S28-Apolymer667474.72UniProt (Q3E7X9)
Pfam (PF01200)		Saccharomyces cerevisiae ATCC 204508 / S288cS33,YS27
31EA, FD
(D9, d9)		40S ribosomal protein S29-Apolymer556544.52UniProt (P41057)
Pfam (PF00253)		Saccharomyces cerevisiae ATCC 204508 / S288cS36,YS29
32FA
(E0)		40S ribosomal protein S30-Apolymer606779.11UniProt (P0CX33)
Pfam (PF04758)		Saccharomyces cerevisiae ATCC 204508 / S288c
33GA, HD
(E1, e1)		Ubiquitin-40S ribosomal protein S31polymer768703.52UniProt (P05759)
Pfam (PF01599)		Saccharomyces cerevisiae ATCC 204508 / S288c
34HA, ID
(SR, sR)		Guanine nucleotide-binding protein subunit beta-like proteinpolymer31834710.02UniProt (P38011)
Pfam (PF00400)		Saccharomyces cerevisiae ATCC 204508 / S288cReceptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
35IA
(SM)		Suppressor protein STM1polymer27330048.01UniProt (P39015)
Pfam (PF09598)		Saccharomyces cerevisiae ATCC 204508 / 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
36JA, KD
(1, 5)		25S ribosomal RNApolymer33961097493.92Saccharomyces cerevisiae ATCC 204508 / S288cRNA (3149-MER)
37KA, LD
(3, 7)		5S ribosomal RNApolymer12138951.12Saccharomyces cerevisiae ATCC 204508 / S288cRNA (121-MER)
38LA, MD
(4, 8)		5.8S ribosomal RNApolymer15850682.92GenBank (618731124)Saccharomyces cerevisiae ATCC 204508 / S288cRNA (158-MER)
39MA, ND
(L2, l2)		60S ribosomal protein L2-Apolymer25327332.42UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)		Saccharomyces cerevisiae ATCC 204508 / S288cL5,RP8,YL6
40NA, OD
(L3, l3)		60S ribosomal protein L3polymer38643719.62UniProt (P14126)
Pfam (PF00297)		Saccharomyces cerevisiae ATCC 204508 / S288cMaintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
41OA, PD
(L4, l4)		60S ribosomal protein L4-Apolymer36139027.92UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)		Saccharomyces cerevisiae ATCC 204508 / S288cL2,RP2,YL2
42PA, QD
(L5, l5)		60S ribosomal protein L5polymer29633633.62UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)		Saccharomyces cerevisiae ATCC 204508 / S288cL1,L1a,Ribosomal 5S RNA-binding protein,YL3
43QA, RD
(L6, l6)		60S ribosomal protein L6-Apolymer17519869.42UniProt (Q02326)
Pfam (PF01159)		Saccharomyces cerevisiae ATCC 204508 / S288cL17,RP18,YL16
44RA, SD
(L7, l7)		60S ribosomal protein L7-Apolymer24327555.12UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)		Saccharomyces cerevisiae ATCC 204508 / S288cL6,RP11,YL8
45SA, TD
(L8, l8)		60S ribosomal protein L8-Apolymer25528044.62UniProt (P17076)
Pfam (PF01248)		Saccharomyces cerevisiae ATCC 204508 / S288cL4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
46TA, UD
(L9, l9)		60S ribosomal protein L9-Apolymer19121605.12UniProt (P05738)
Pfam (PF00347)		Saccharomyces cerevisiae ATCC 204508 / S288cL8,RP24,YL11
47UA, VD
(M0, m0)		60S ribosomal protein L10polymer22025279.32UniProt (P41805)
Pfam (PF00252)		Saccharomyces cerevisiae ATCC 204508 / S288cL9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
48VA, WD
(M1, m1)		60S ribosomal protein L11-Bpolymer17319654.52UniProt (Q3E757)
Pfam (PF00281)
Pfam (PF00673)		Saccharomyces cerevisiae ATCC 204508 / S288cL16,RP39,YL22
49WA, YD
(M3, m3)		60S ribosomal protein L13-Apolymer19822473.02UniProt (Q12690)
Pfam (PF01294)		Saccharomyces cerevisiae ATCC 204508 / S288c
50XA, ZD
(M4, m4)		60S ribosomal protein L14-Apolymer13715063.92UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)		Saccharomyces cerevisiae ATCC 204508 / S288c
51AE, YA
(M5, m5)		60S ribosomal protein L15-Apolymer20324351.22UniProt (P05748)
Pfam (PF00827)		Saccharomyces cerevisiae ATCC 204508 / S288cL13,RP15R,YL10,YP18
52BE, ZA
(M6, m6)		60S ribosomal protein L16-Apolymer19822116.02UniProt (P26784)
Pfam (PF00572)		Saccharomyces cerevisiae ATCC 204508 / S288cL13a,L21,RP22,YL15
53AB, CE
(M7, m7)		60S ribosomal protein L17-Apolymer18320458.32UniProt (P05740)
Pfam (PF00237)		Saccharomyces cerevisiae ATCC 204508 / S288cL20A,YL17
54BB, DE
(M8, m8)		60S ribosomal protein L18-Apolymer18520478.12UniProt (P0CX49)
Pfam (PF17135)		Saccharomyces cerevisiae ATCC 204508 / S288cRP28
55CB, EE
(M9, m9)		60S ribosomal protein L19-Apolymer18821631.12UniProt (P0CX82)
Pfam (PF01280)
Pfam (PF25476)		Saccharomyces cerevisiae ATCC 204508 / S288cL23,RP15L,RP33,YL14
56DB, FE
(N0, n0)		60S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)		Saccharomyces cerevisiae ATCC 204508 / S288cL18a
57EB, GE
(N1, n1)		60S ribosomal protein L21-Apolymer15918148.12UniProt (Q02753)
Pfam (PF01157)		Saccharomyces cerevisiae ATCC 204508 / S288c
58FB, HE
(N2, n2)		60S ribosomal protein L22-Apolymer12013580.22UniProt (P05749)
Pfam (PF01776)		Saccharomyces cerevisiae ATCC 204508 / S288cL1c,RP4,YL31
59GB, IE
(N3, n3)		60S ribosomal protein L23-Apolymer13614362.82UniProt (P0CX41)
Pfam (PF00238)		Saccharomyces cerevisiae ATCC 204508 / S288cL17a,YL32
60HB, JE
(N4, n4)		60S ribosomal protein L24-Apolymer15517661.72UniProt (P04449)
Pfam (PF01246)		Saccharomyces cerevisiae ATCC 204508 / S288cL30,RP29,YL21
61IB, KE
(N5, n5)		60S ribosomal protein L25polymer14115656.42UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)		Saccharomyces cerevisiae ATCC 204508 / S288cRP16L,YL25,YP42'
62JB, LE
(N6, n6)		60S ribosomal protein L26-Apolymer12614134.62UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)		Saccharomyces cerevisiae ATCC 204508 / S288cL33,YL33
63KB, ME
(N7, n7)		60S ribosomal protein L27-Apolymer13515437.22UniProt (P0C2H6)
Pfam (PF01777)		Saccharomyces cerevisiae ATCC 204508 / S288c
64LB, NE
(N8, n8)		60S ribosomal protein L28polymer14816630.52UniProt (P02406)
Pfam (PF00828)		Saccharomyces cerevisiae ATCC 204508 / S288cL27a,L29,RP44,RP62,YL24
65MB, OE
(N9, n9)		60S ribosomal protein L29polymer586560.72UniProt (P05747)
Pfam (PF01779)		Saccharomyces cerevisiae ATCC 204508 / S288cYL43
66NB, PE
(O0, o0)		60S ribosomal protein L30polymer10411299.22UniProt (P14120)
Pfam (PF01248)		Saccharomyces cerevisiae ATCC 204508 / S288cL32,RP73,YL38
67OB, QE
(O1, o1)		60S ribosomal protein L31-Apolymer11212849.02UniProt (P0C2H8)
Pfam (PF01198)		Saccharomyces cerevisiae ATCC 204508 / S288cL34,YL28
68PB, RE
(O2, o2)		60S ribosomal protein L32polymer12914678.22UniProt (P38061)
Pfam (PF01655)		Saccharomyces cerevisiae ATCC 204508 / S288c
69QB, SE
(O3, o3)		60S ribosomal protein L33-Apolymer10612045.92UniProt (P05744)
Pfam (PF01247)		Saccharomyces cerevisiae ATCC 204508 / S288cL37,RP47,YL37
70RB, TE
(O4, o4)		60S ribosomal protein L34-Apolymer11913412.82UniProt (P87262)
Pfam (PF01199)		Saccharomyces cerevisiae ATCC 204508 / S288c
71SB, UE
(O5, o5)		60S ribosomal protein L35-Apolymer11913811.42UniProt (P0CX84)
Pfam (PF00831)		Saccharomyces cerevisiae ATCC 204508 / S288c
72TB, VE
(O6, o6)		60S ribosomal protein L36-Apolymer9911020.12UniProt (P05745)
Pfam (PF01158)		Saccharomyces cerevisiae ATCC 204508 / S288cL39,YL39
73UB, WE
(O7, o7)		60S ribosomal protein L37-Apolymer879746.22UniProt (P49166)
Pfam (PF01907)		Saccharomyces cerevisiae ATCC 204508 / S288cL43,YL35,YP55
74VB, XE
(O8, o8)		60S ribosomal protein L38polymer778714.42UniProt (P49167)
Pfam (PF01781)		Saccharomyces cerevisiae ATCC 204508 / S288c
75WB, YE
(O9, o9)		60S ribosomal protein L39polymer506227.42UniProt (P04650)
Pfam (PF00832)		Saccharomyces cerevisiae ATCC 204508 / S288cL46,YL40
76XB, ZE
(Q0, q0)		Ubiquitin-60S ribosomal protein L40polymer526032.32UniProt (P0CH08)
Pfam (PF01020)		Saccharomyces cerevisiae ATCC 204508 / S288c
77AF, YB
(Q1, q1)		60S ribosomal protein L41-Apolymer253354.22UniProt (P0CX86)
Pfam (PF05162)		Saccharomyces cerevisiae ATCC 204508 / S288cL47,YL41
78BF, ZB
(Q2, q2)		60S ribosomal protein L42-Apolymer10512115.52UniProt (P0CX27)
Pfam (PF00935)		Saccharomyces cerevisiae ATCC 204508 / S288cL41,YL27,YP44
79AC, CF
(Q3, q3)		60S ribosomal protein L43-Apolymer919981.82UniProt (P0CX25)
Pfam (PF01780)		Saccharomyces cerevisiae ATCC 204508 / S288cL37a,YL35
80GD
(e0)		40S ribosomal protein S30-Apolymer627006.31UniProt (P0CX33)
Pfam (PF04758)		Saccharomyces cerevisiae ATCC 204508 / S288c
81JD
(sM)		Suppressor protein STM1polymer27330076.11UniProt (P39015)
Pfam (PF09598)		Saccharomyces cerevisiae ATCC 204508 / 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
82XD
(m2)		unknown protein chain m2polymer16013634.81PDB (4U53)Saccharomyces cerevisiae ATCC 204508 / S288c
83DF
(p0)		60S acidic ribosomal protein P0polymer31133617.91UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Pfam (PF00428)		Saccharomyces cerevisiae ATCC 204508 / S288c
84EF
(p1)		unknown protein chain p1polymer474017.91PDB (4U53)Saccharomyces cerevisiae ATCC 204508 / S288c
85FF
(p2)		unknown protein chain p2polymer463932.81PDB (4U53)Saccharomyces cerevisiae ATCC 204508 / S288c
86AAA, AAC, ABA, ABB, ABC...
(1, 5, Q2, 6, 2...)		MAGNESIUM IONnon-polymer24.31412Chemie (MG)
PubChem (888)
87AAB, AHB, AIB, AIC, AJA...
(M7, 6, 5, 1, 2...)		osmium (III) hexamminenon-polymer286.41133Chemie (OHX)
88CBB, LQ, LZC, MQ, NQ...
(Q3, D6, o7, D7, D9...)		ZINC IONnon-polymer65.416Chemie (ZN)
89DWA, UUC
(1, 5)		(1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diolnon-polymer287.32Chemie (3KD)
PubChem (3978)
PubChem (72378)
PubChem (40468048)
PubChem (40469622)
PubChem (45489001)
PubChem (667419)
PubChem (51380971)
PubChem (5319129)
PubChem (6540810)
PubChem (6602494)
PubChem (6604308)
PubChem (7060909)
PubChem (11822288)
PubChem (12305849)
PubChem (12305850)
PubChem (6713967)
PubChem (124300586)
PubChem (137705777)
PubChem (162880197)
Sequence modifications
C0, c0: 1 - 105 (UniProt: Q08745)
PDBExternal DatabaseDetails
Ala 89Gly 89conflict
C1, c1: 2 - 156 (UniProt: P0CX47)
PDBExternal DatabaseDetails
Ala 147Gly 147conflict
C2, c2: 2 - 143 (UniProt: P48589)
PDBExternal DatabaseDetails
Ala 104Gly 104conflict
Ala 110Gly 110conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains162
Total formula weight6271202.7
Non-Polymers*Number of molecules2563
Total formula weight360391.4
All*Total formula weight6631594.1
*Water molecules are not included.

251422

PDB entries from 2026-04-01

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