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9NJF

E. coli pre-elongation complex without an A-site tRNA with EQ2-YbiT in Non-hydrolytic 1/PtIM(a) conformation

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(1)
Large ribosomal subunit protein uL1polymer22023392.11UniProt (P0A7L0)
Pfam (PF00687)
Escherichia coli50S ribosomal protein L1
2B
(10)
Large ribosomal subunit protein uL10polymer13114112.31UniProt (P0A7J3)
Pfam (PF00466)
Escherichia coli50S ribosomal protein L10,50S ribosomal protein L8
3C
(11)
Large ribosomal subunit protein uL11polymer14114763.21UniProt (P0A7J7)
Pfam (PF03946)
Pfam (PF00298)
Escherichia coli50S ribosomal protein L11
4D
(13)
Large ribosomal subunit protein uL13polymer14216050.61UniProt (P0AA10)
Pfam (PF00572)
Escherichia coli50S ribosomal protein L13
5E
(14)
Large ribosomal subunit protein uL14polymer12313565.11UniProt (P0ADY3)
Pfam (PF00238)
Escherichia coli50S ribosomal protein L14
6F
(15)
50S ribosomal protein L15polymer14314877.31UniProt (A0A037Y8L6)
Pfam (PF00828)
UniProt (by SIFTS) (P02413)
Escherichia coli
7G
(16)
50S ribosomal protein L16polymer13615312.31UniProt (P0ADY7)
Pfam (PF00252)
Escherichia coliLarge ribosomal subunit protein uL16
8H
(17)
Large ribosomal subunit protein bL17polymer12013721.91UniProt (P0AG44)
Pfam (PF01196)
Escherichia coli50S ribosomal protein L17
9I
(18)
Large ribosomal subunit protein uL18polymer11612663.51UniProt (P0C018)
Pfam (PF00861)
Escherichia coli50S ribosomal protein L18
10J
(19)
50S ribosomal protein L19polymer11413028.11UniProt (S1PSA3)
Pfam (PF01245)
UniProt (by SIFTS) (P0A7K6)
Escherichia coli
11K
(2)
50S ribosomal protein L2polymer27129663.21UniProt (P60422)
Pfam (PF00181)
Pfam (PF03947)
Escherichia coliLarge ribosomal subunit protein uL2
12L
(20)
Large ribosomal subunit protein bL20polymer11713396.81UniProt (C3T7Q7)Escherichia coli
13M
(21)
Large ribosomal subunit protein bL21polymer10311586.41UniProt (Q1R6F0)
Pfam (PF00829)
UniProt (by SIFTS) (P0AG48)
Escherichia coli50S ribosomal protein L21
14N
(22)
Large ribosomal subunit protein uL22polymer11012253.41UniProt (Q1R610)
Pfam (PF00237)
UniProt (by SIFTS) (P61175)
Escherichia coli50S ribosomal protein L22
15O
(23)
Large ribosomal subunit protein uL23polymer9310546.51UniProt (C3SQV2)
Pfam (PF00276)
UniProt (by SIFTS) (P0ADZ0)
Escherichia coli
16P
(24)
Large ribosomal subunit protein uL24polymer10211078.91UniProt (A0A7U9LWC1)
Pfam (PF00467)
Pfam (PF17136)
UniProt (by SIFTS) (P60624)
Escherichia coli50S ribosomal protein L24
17Q
(25)
Large ribosomal subunit protein bL25polymer9410713.51UniProt (P68919)
Pfam (PF01386)
Escherichia coli
18R
(27)
50S ribosomal protein L27polymer758174.41UniProt (A0A1X3JCC7)
Pfam (PF01016)
UniProt (by SIFTS) (P0A7L8)
Escherichia coli
19S
(28)
50S ribosomal protein L28polymer778896.41UniProt (A0A0E2KZD0)
Pfam (PF00830)
UniProt (by SIFTS) (P0A7M2)
Escherichia coli
20T
(29)
Large ribosomal subunit protein uL29polymer637286.51UniProt (C3SQY2)
Pfam (PF00831)
UniProt (by SIFTS) (P0A7M6)
Escherichia coli
21U
(3)
50S ribosomal protein L3polymer20922277.51UniProt (P60438)
Pfam (PF00297)
Escherichia coliLarge ribosomal subunit protein uL3
22V
(30)
50S ribosomal protein L30polymer586423.61UniProt (P0AG51)
Pfam (PF00327)
Escherichia coliLarge ribosomal subunit protein uL30
23W
(31)
Large ribosomal subunit protein bL31polymer667516.71UniProt (P0A7M9)
Pfam (PF01197)
Escherichia coli50S ribosomal protein L31
24X
(32)
50S ribosomal protein L32polymer566332.21UniProt (A0A828UBL8)
Pfam (PF01783)
UniProt (by SIFTS) (P0A7N4)
Escherichia coli
25Y
(33)
Large ribosomal subunit protein bL33polymer505814.81UniProt (P0A7N9)
Pfam (PF00471)
Escherichia coli50S ribosomal protein L33
26Z
(34)
50S ribosomal protein L34polymer465397.51UniProt (B7MGC4)
Pfam (PF00468)
UniProt (by SIFTS) (P0A7P5)
Escherichia coli
27AA
(35)
Large ribosomal subunit protein bL35polymer647181.81UniProt (P0A7Q2)
Pfam (PF01632)
UniProt (by SIFTS) (P0A7Q1)
Escherichia coli
28BA
(36)
50S ribosomal protein L36polymer384377.41UniProt (A0A0E2L017)
Pfam (PF00444)
UniProt (by SIFTS) (P0A7Q6)
Escherichia coli
29CA
(4)
Large ribosomal subunit protein uL4polymer20122121.61UniProt (P60723)
Pfam (PF00573)
Escherichia coli50S ribosomal protein L4
30DA
(5)
50S ribosomal protein L5polymer17720073.21UniProt (A0A4P8BX24)
Pfam (PF00281)
Pfam (PF00673)
UniProt (by SIFTS) (P62399)
Escherichia coli
31EA
(6)
Large ribosomal subunit protein uL6polymer17618801.61UniProt (C3SR17)
Pfam (PF00347)
UniProt (by SIFTS) (P0AG55)
Escherichia coli
32FA
(9)
Large ribosomal subunit protein bL9polymer14915789.01UniProt (P0A7R1)
Pfam (PF01281)
Pfam (PF03948)
Escherichia coli50S ribosomal protein L9
33GA
(M)
mRNApolymer61900.21Escherichia coli
34HA
(R1)
23S ribosomal RNApolymer2903941322.21GenBank (2019144442)Escherichia coli
35IA
(R2)
5S ribosomal RNApolymer11938483.91GenBank (1815787944)Escherichia coli
36JA
(R3)
16S ribosomal RNApolymer1538498420.21GenBank (2044032419)Escherichia coli
37KA
(T)
tRNApolymer7624506.61GenBank (1845258627)Escherichia coli
38LA
(Y)
Probable ATP-binding protein YbiTpolymer53059924.91UniProt (P0A9U3)
Pfam (PF00005)
Pfam (PF12848)
Escherichia coli
39MA
(sb)
Small ribosomal subunit protein uS2polymer21824253.91UniProt (P0A7V0)
Pfam (PF00318)
Escherichia coli30S ribosomal protein S2
40NA
(sc)
Small ribosomal subunit protein uS3polymer20623078.81UniProt (P0A7V5)
Pfam (PF07650)
Pfam (PF00189)
UniProt (by SIFTS) (P0A7V3)
Escherichia coli30S ribosomal protein S3
41OA
(sd)
30S ribosomal protein S4polymer20523383.01UniProt (C3SR62)
Pfam (PF00163)
Pfam (PF01479)
UniProt (by SIFTS) (P0A7V8)
Escherichia coli
42PA
(se)
Small ribosomal subunit protein uS5polymer15716532.11UniProt (P0A7W1)
Pfam (PF00333)
Pfam (PF03719)
Escherichia coli30S ribosomal protein S5
43QA
(sf)
30S ribosomal protein S6, non-modified isoformpolymer10011669.41UniProt (P02358)
Pfam (PF01250)
Escherichia coli
44RA
(sg)
30S ribosomal protein S7polymer15116861.51UniProt (P02359)
Pfam (PF00177)
Escherichia coliSmall ribosomal subunit protein uS7
45SA
(sh)
30S ribosomal protein S8polymer12914015.41UniProt (A0A828U358)
Pfam (PF00410)
UniProt (by SIFTS) (P0A7W7)
Escherichia coli
46TA
(si)
Small ribosomal subunit protein uS9polymer12714554.91UniProt (C3SRY2)
Pfam (PF00380)
UniProt (by SIFTS) (P0A7X3)
Escherichia coli
47UA
(sj)
30S ribosomal protein S10polymer9811197.01UniProt (A0A0H3EQD3)
Pfam (PF00338)
UniProt (by SIFTS) (P0A7R5)
Escherichia coli
48VA
(sk)
Small ribosomal subunit protein uS11polymer11612388.11UniProt (C3SR57)
Pfam (PF00411)
UniProt (by SIFTS) (P0A7R9)
Escherichia coli
49WA
(sl)
Small ribosomal subunit protein uS12polymer12313637.01UniProt (C3SQR7)
Pfam (PF00164)
UniProt (by SIFTS) (P0A7S3)
Escherichia coli
50XA
(sm)
30S ribosomal protein S13polymer11412625.81UniProt (S1P5F8)
Pfam (PF00416)
UniProt (by SIFTS) (P0A7S9)
Escherichia coli
51YA
(sn)
Small ribosomal subunit protein uS14polymer10011475.41UniProt (A0A8S0FJJ0)
Pfam (PF00253)
UniProt (by SIFTS) (P0AG59)
Escherichia coli
52ZA
(so)
Small ribosomal subunit protein uS15polymer8810159.61UniProt (P0ADZ4)
Pfam (PF00312)
Escherichia coli30S ribosomal protein S15
53AB
(sp)
Small ribosomal subunit protein bS16polymer829207.61UniProt (C3SYP2)
Pfam (PF00886)
UniProt (by SIFTS) (P0A7T3)
Escherichia coli
54BB
(sq)
Small ribosomal subunit protein uS17polymer809263.91UniProt (P0AG63)
Pfam (PF00366)
Escherichia coli30S ribosomal protein S17
55CB
(sr)
30S ribosomal protein S18polymer657606.81UniProt (E0J6I2)
Pfam (PF01084)
UniProt (by SIFTS) (P0A7T7)
Escherichia coli
56DB
(ss)
30S ribosomal protein S19polymer799057.61UniProt (A0A7U9LGZ0)
Pfam (PF00203)
UniProt (by SIFTS) (P0A7U3)
Escherichia coli
57EB
(st)
30S ribosomal protein S20polymer859506.21UniProt (C3TRH7)
Pfam (PF01649)
UniProt (by SIFTS) (P0A7U7)
Escherichia coli
58FB
(su)
Small ribosomal subunit protein bS21polymer657763.11UniProt (P68679)
Pfam (PF01165)
Escherichia coli30S ribosomal protein S21
59AC, AD, AE, AF, AG...
(R1, R3, 18, 32, 33...)
MAGNESIUM IONnon-polymer24.3124Chemie (MG)
60JB
(36)
ZINC IONnon-polymer65.41Chemie (ZN)
61BG, CG
(Y)
ADENOSINE-5'-TRIPHOSPHATEnon-polymer507.22Chemie (ATP)
62DG, EG
(Y)
SODIUM IONnon-polymer23.02Chemie (NA)
Sequence modifications
R1: 1 - 2903 (GenBank: 2019144442)
PDBExternal DatabaseDetails
G 1847A 2609611conflict
T: 1 - 76 (GenBank: 1845258627)
PDBExternal DatabaseDetails
A 34U 666844conflict
Y: 1 - 530 (UniProt: P0A9U3)
PDBExternal DatabaseDetails
Gln 181Glu 181conflict
Gln 464Glu 464conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains58
Total formula weight2249984.0
Non-Polymers*Number of molecules129
Total formula weight4139.6
All*Total formula weight2254123.6
*Water molecules are not included.

239149

PDB entries from 2025-07-23

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