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SMTL ID : 7bl5.1

pre-50S-ObgE particle

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Covalent)

GDP.1:

21 residues within 4Å:

Chain 2: M.167, P.168, N.169, A.170, G.171, K.172, S.173, T.174, V.186, A.187, D.188, Y.189, T.192, N.283, K.284, D.286, L.287, S.314, A.315, A.316
Ligands: MG.2

17 PLIP interactions:

17 interactions with chain 2

Hydrogen bonds: 2:A.170, 2:G.171, 2:K.172, 2:S.173, 2:T.174, 2:T.174, 2:A.187, 2:T.192, 2:T.192, 2:N.283, 2:K.284, 2:K.284, 2:A.315, 2:A.316
Salt bridges: 2:K.172, 2:D.286
pi-Cation interactions: 2:K.284

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2:	3 residues within 4Å: Chain 2: K.172, S.173 Ligands: GDP.1 1 PLIP interactions: 1 interactions with chain 2 Metal complexes: 2:S.173
MG.3:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.4:

5 residues within 4Å:

Chain 8: C.16, C.18, V.36, C.37, C.40

4 PLIP interactions:

4 interactions with chain 8

Metal complexes: 8:C.16, 8:C.18, 8:C.37, 8:C.40

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Nikolay, R. et al., Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization. Mol.Cell (2021)

Release Date

2021-05-12

Peptides

50S ribosomal protein L2: A
50S ribosomal protein L3: B
50S ribosomal protein L4: C
50S ribosomal protein L6: D
50S ribosomal protein L13: E
50S ribosomal protein L15: F
50S ribosomal protein L17: G
50S ribosomal protein L18: H
50S ribosomal protein L20: I
50S ribosomal protein L21: J
50S ribosomal protein L22: K
50S ribosomal protein L23: L
50S ribosomal protein L24: M
50S ribosomal protein L25: N
50S ribosomal protein L27: O
50S ribosomal protein L28: P
50S ribosomal protein L29: Q
50S ribosomal protein L30: R
50S ribosomal protein L32: S
50S ribosomal protein L33: T
50S ribosomal protein L34: U
50S ribosomal protein L11: W
50S ribosomal protein L14: X
50S ribosomal protein L19: Y
Ribosomal silencing factor RsfS: Z
Ribosomal large subunit pseudouridine synthase D: 0
UPF0307 protein YjgA: 1
GTPase ObgE/CgtA: 2
50S ribosomal protein L16: 3
50S ribosomal protein L9: 5
50S ribosomal protein L10: 6
50S ribosomal protein L5: 7
50S ribosomal protein L31: 8

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
G

E
J

F
L

G
N

H
O

I
Q

J
R

K
S

L
T

M
U

N
V

O
W

P
X

Q
Y

R
Z

S
0

T
1

U
2

W
I

X
K

Y
P

Z
6

0
7

1
8

2
9

3
M

5
H

6
e

7
F

8
b

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

50S ribosomal protein L2

50S ribosomal protein L3

50S ribosomal protein L4

50S ribosomal protein L6

50S ribosomal protein L13

50S ribosomal protein L15

50S ribosomal protein L17

50S ribosomal protein L18

50S ribosomal protein L20

50S ribosomal protein L21

50S ribosomal protein L22

50S ribosomal protein L23

50S ribosomal protein L24

50S ribosomal protein L25

50S ribosomal protein L27

50S ribosomal protein L28

50S ribosomal protein L29

50S ribosomal protein L30

50S ribosomal protein L32

50S ribosomal protein L33

50S ribosomal protein L34

50S ribosomal protein L11

50S ribosomal protein L14

50S ribosomal protein L19

Ribosomal silencing factor RsfS

Ribosomal large subunit pseudouridine synthase D

UPF0307 protein YjgA

GTPase ObgE/CgtA

50S ribosomal protein L16

50S ribosomal protein L9

50S ribosomal protein L10

50S ribosomal protein L5

50S ribosomal protein L31

Related Entries With Identical Sequence

1b75.1 | 1d6k.1 | 1dfu.1 | 2j28.1 | 3bbx.1 | 3j45.1 | 3j46.1 | 3j5l.1 | 3j7z.1 | 3j8g.1 | 3j9y.1 | 3j9z.1 | 3ja1.1 | 3jbu.1 | 3jbv.1 | 3jcd.1 | 3jce.1 | 3jcj.1 | 3jcn.1 | 487d.1 | 4csu.1 | 4peb.1 | 4pec.1 | 4tom.1 | 4too.1 | 4tov.1 | 4tox.1 | 4tp1.1 | 4tp3.1 | 4tp5.1 more...less...

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4woi.2 | 4www.1 | 4www.2 | 4ybb.1 | 4ybb.2 | 5ady.1 | 5afi.1 | 5aka.1 | 5gad.1 | 5gae.1 | 5gaf.1 | 5gag.1 | 5gah.1 | 5h5u.1 | 5iqr.1 | 5it8.1 | 5it8.2 | 5j5b.1 | 5j5b.2 | 5j7l.1 | 5j7l.2 | 5j88.1 | 5j88.2 | 5j8a.1 | 5j8a.2 | 5j91.1 | 5j91.2 | 5jc9.1 | 5jc9.2 | 5jte.1 | 5ju8.1 | 5kcr.1 | 5kcs.1 | 5kps.1 | 5kpv.1 | 5kpw.1 | 5kpx.1 | 5l3p.1 | 5lza.1 | 5lzb.1 | 5lzc.1 | 5lzd.1 | 5lze.1 | 5lzf.1 | 5mdv.1 | 5mdw.1 | 5mdy.1 | 5mdz.1 | 5mgp.1 | 5nco.1 | 5np6.1 | 5nwy.1 | 5o2r.1 | 5u4i.1 | 5u9f.1 | 5u9g.1 | 5uyk.1 | 5uyl.1 | 5uym.1 | 5uyn.1 | 5uyp.1 | 5uyq.1 | 5wdt.1 | 5we4.1 | 5we6.1 | 5wf0.1 | 5wfk.1 | 5wfs.1 | 6bu8.1 | 6by1.1 | 6by1.2 | 6c4h.1 | 6c4i.1 | 6dnc.1 | 6enf.1 | 6enj.1 | 6enu.1 | 6gbz.1 | 6gc0.1 | 6gc4.1 | 6gc6.1 | 6gc7.1 | 6gc8.1 | 6gwt.1 | 6gxm.1 | 6gxn.1 | 6gxo.1 | 6gxp.1 | 6h4n.1 | 6h58.3 | 6h58.8 | 6h58.9 | 6h58.12 | 6h58.13 | 6h58.16 | 6h58.21 | 6h58.22 | 6h58.25 | 6h58.28 | 6h58.55 | 6h58.60 | 6h58.61 | 6h58.64 | 6h58.65 | 6h58.68 | 6h58.73 | 6h58.74 | 6h58.77 | 6h58.80 | 6hrm.1 | 6i0y.1 | 6i7v.42 | 6i7v.43 | 6i7v.48 | 6i7v.49 | 6i7v.50 | 6i7v.51 | 6i7v.53 | 6i7v.56 | 6i7v.57 | 6i7v.60 | 6i7v.67 | 6i7v.71 | 6i7v.72 | 6i7v.77 | 6i7v.78 | 6i7v.79 | 6i7v.80 | 6i7v.82 | 6i7v.85 | 6i7v.86 | 6i7v.89 | 6i7v.96 | 6lkq.1 | 6o9j.1 | 6o9k.1 | 6ofx.1 | 6og7.1 | 6ogf.1 | 6ogg.1 | 6ogi.1 | 6om6.1 | 6ore.1 | 6orl.1 | 6osk.1 | 6osq.1 | 6ost.1 | 6ot3.1 | 6ouo.1 | 6pc5.1 | 6pc6.1 | 6pc7.1 | 6pc8.1 | 6pch.1 | 6pcq.1 | 6pcr.1 | 6pcs.1 | 6pct.1 | 6pj6.1 | 6q97.1 | 6q98.1 | 6q9a.1 | 6qdw.1 | 6qul.1 | 6s0k.1 | 6szs.1 | 6tbv.1 | 6tc3.1 | 6u48.1 | 6vwl.1 | 6vwm.1 | 6vwn.1 | 6vyx.1 | 6vyx.2 | 6vyx.3 | 6vyx.4 | 6vyx.5 | 6vyx.33 | 6vyx.34 | 6vyx.35 | 6vyx.36 | 6vyx.37 | 6vyx.38 | 6vyx.39 | 6vyx.40 | 6vyx.41 | 6vyx.42 | 6vyx.43 | 6vyx.44 | 6vyx.46 | 6vyx.48 | 6vyx.49 | 6vyx.50 | 6vyx.51 | 6vyx.52 | 6vyx.54 | 6vyx.55 | 6vyx.56 | 6vz3.1 | 6vz3.2 | 6vz3.5 | 6vz3.40 | 6vz3.42 | 6vz3.43 | 6vz3.48 | 6vz3.49 | 6vz3.50 | 6vz3.51 | 6vz3.52 | 6wd0.1 | 6wd1.1 | 6wd2.1 | 6wd3.1 | 6wd4.1 | 6wd5.1 | 6wd6.1 | 6wd7.1 | 6wd8.1 | 6wd9.1 | 6wda.1 | 6wdb.1 | 6wdc.1 | 6wdd.1 | 6wde.1 | 6wdf.1 | 6wdg.1 | 6wdh.1 | 6wdi.1 | 6wdj.1 | 6wdk.1 | 6wdl.1 | 6wdm.1 | 6wnt.1 | 6wnv.1 | 6wnw.1 | 6wyv.1 | 6xz7.1 | 6xza.1 | 6xzb.1 | 6y69.1 | 6ys3.1 | 6ysr.1 | 6yss.1 | 6yst.1 | 6ysu.1 | 6ztj.22 | 6ztj.23 | 6ztj.24 | 6ztj.25 | 6ztj.26 | 6ztj.27 | 6ztj.28 | 6ztj.29 | 6ztj.30 | 6ztj.31 | 6ztj.34 | 6ztj.35 | 6ztj.36 | 6ztj.37 | 6ztj.38 | 6ztj.39 | 6ztj.40 | 6ztj.41 | 6ztj.42 | 6ztj.43 | 6ztj.44 | 6ztj.45 | 6ztj.46 | 6ztj.47 | 6ztj.48 | 6ztj.49 | 6ztj.52 | 6ztl.1 | 6ztm.1 | 6ztn.21 | 6ztn.22 | 6ztn.23 | 6ztn.24 | 6ztn.25 | 6ztn.26 | 6ztn.27 | 6ztn.28 | 6ztn.31 | 6ztn.32 | 6ztn.33 | 6ztn.34 | 6ztn.35 | 6ztn.36 | 6ztn.37 | 6ztn.38 | 6ztn.39 | 6ztn.40 | 6ztn.41 | 6ztn.42 | 6ztn.43 | 6ztn.44 | 6ztn.45 | 6ztn.46 | 6zto.1 | 6ztp.1 | 6zu1.1 | 7abz.1 | 7ac7.1 | 7acj.1 | 7acr.1 | 7b5k.1 | 7bl2.1 | 7bl3.1 | 7bl4.1 | 7bl6.1 | 7bv8.1 | 7cpj.1 | 7d6z.1 | 7d80.1 | 7jss.1 | 7jsw.1 | 7jsz.1 | 7jt1.1 | 7jt2.1 | 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9ha1.1 | 9ha2.1 | 9ha3.1 | 9ha4.1 | 9ha5.1 | 9ha6.1 | 9ha7.1 | 9hai.1 | 9hal.1 | 9ham.1 | 9mor.1 | 9mq4.1

Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

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