SMTL ID : 8rl2.1

Human pre-60S - State 5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain 5: S.44, C.46, C.49, C.83, C.86 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.46, 5:C.49, 5:C.83, 5:C.86 ZN.2: 4 residues within 4Å: Chain 8: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain 8 Metal complexes: 8:C.19, 8:C.22, 8:C.34, 8:C.37 ZN.3: 4 residues within 4Å: Chain b: C.39, C.42, C.57, C.60 4 PLIP interactions: 4 interactions with chain b Metal complexes: b:C.39, b:C.42, b:C.57, b:C.60 ZN.8: 4 residues within 4Å: Chain m: C.6, C.9, C.32, C.36 4 PLIP interactions: 4 interactions with chain m Metal complexes: m:C.6, m:C.9, m:C.32, m:C.36 ZN.9: 4 residues within 4Å: Chain p: C.63, C.66, H.79, H.85 4 PLIP interactions: 4 interactions with chain p Metal complexes: p:C.63, p:C.66, p:H.79, p:H.85

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.4: 23 residues within 4Å: Ligands: MG.5 Chain f: N.255, K.256, D.258, L.259, H.282, A.283, P.319, N.320, V.321, G.322, K.323, S.324, S.325, V.338, A.339, P.340, I.341, A.342, G.343, E.344, T.345 Chain n: R.279 22 PLIP interactions: 22 interactions with chain f Hydrogen bonds: f:N.255, f:K.256, f:K.256, f:H.282, f:A.283, f:N.320, f:V.321, f:G.322, f:K.323, f:S.324, f:S.324, f:S.325, f:S.325, f:A.339, f:A.339, f:G.343, f:E.344, f:T.345, f:T.345 Salt bridges: f:D.258, f:K.323, f:K.323

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Ligands: GTP.4 Chain f: N.320, A.339, P.340, I.341 2 PLIP interactions: 2 interactions with chain f Metal complexes: f:A.339, f:I.341 MG.7: 3 residues within 4Å: Ligands: GDP.6 Chain h: S.182, T.202 2 PLIP interactions: 2 interactions with chain h Metal complexes: h:S.182, h:T.202

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.6: 19 residues within 4Å: Ligands: MG.7 Chain h: Y.176, P.177, N.178, V.179, G.180, K.181, S.182, S.183, V.195, Q.196, P.197, N.289, K.290, D.292, V.293, S.321, T.322, L.323 13 PLIP interactions: 13 interactions with chain h Hydrogen bonds: h:V.179, h:G.180, h:K.181, h:S.182, h:S.183, h:S.183, h:Q.196, h:N.289, h:K.290, h:K.290, h:T.322 Salt bridges: h:K.181, h:D.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoms, M. et al., Human pre-60S - State 5. To Be Published

Release Date

2025-01-15

Peptides

60S ribosomal protein L8: D
60S ribosomal protein L3: E
60S ribosomal protein L4: F
60S ribosomal protein L5: G
60S ribosomal protein L6: H
60S ribosomal protein L7: I
60S ribosomal protein L7a: J
60S ribosomal protein L9: K
60S ribosomal protein L11: L
60S ribosomal protein L13: M
60S ribosomal protein L14: N
60S ribosomal protein L15: O
60S ribosomal protein L13a: P
60S ribosomal protein L17: Q
60S ribosomal protein L18: R
60S ribosomal protein L19: S
60S ribosomal protein L18a: T
60S ribosomal protein L21: U
60S ribosomal protein L22: V
60S ribosomal protein L23: W
60S ribosomal protein L23a: X
60S ribosomal protein L26: Y
60S ribosomal protein L27: Z
60S ribosomal protein L27a: 0
60S ribosomal protein L30: 1
60S ribosomal protein L31: 2
60S ribosomal protein L32: 3
60S ribosomal protein L35a: 4
60S ribosomal protein L34: 5
60S ribosomal protein L35: 6
60S ribosomal protein L36: 7
60S ribosomal protein L37: 8
60S ribosomal protein L38: 9
60S ribosomal protein L39: a
60S ribosomal protein L37a: b
60S ribosomal protein L28: c
Large ribosomal subunit protein uL11: d
Eukaryotic translation initiation factor 6: e
Nucleolar GTP-binding protein 2: f
Guanine nucleotide-binding protein-like 3: g
GTP-binding protein 4: h
Protein LLP homolog: i
mRNA turnover protein 4 homolog: j
Notchless protein homolog 1: k
Ribosome biogenesis protein NSA2 homolog: l
Probable ribosome biogenesis protein RLP24: m
Ribosome production factor 2 homolog: n
Ribosome biogenesis regulatory protein homolog: o
Zinc finger protein 593: p

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
LA

E
LB

F
LC

G
LD

H
LE

I
LF

J
LG

K
LH

L
LJ

M
LL

N
LM

O
LN

P
LO

Q
LP

R
LQ

S
LR

T
LS

U
LT

V
LU

W
LV

X
LX

Y
LY

Z
LZ

0
La

1
Lc

2
Ld

3
Le

4
Lf

5
Lg

6
Lh

7
Li

8
Lj

9
Lk

a
Ll

b
Lp

c
Lr

d
Lt

e
CA

f
CB

g
CC

h
CD

i
CE

j
CF

k
CG

l
CH

m
CI

n
CJ

o
CK

p
CL

60S ribosomal protein L8

60S ribosomal protein L3

60S ribosomal protein L4

60S ribosomal protein L5

60S ribosomal protein L6

60S ribosomal protein L7

60S ribosomal protein L7a

60S ribosomal protein L9

60S ribosomal protein L11

60S ribosomal protein L13

60S ribosomal protein L14

60S ribosomal protein L15

60S ribosomal protein L13a

60S ribosomal protein L17

60S ribosomal protein L18

60S ribosomal protein L19

60S ribosomal protein L18a

60S ribosomal protein L21

60S ribosomal protein L22

60S ribosomal protein L23

60S ribosomal protein L23a

60S ribosomal protein L26

60S ribosomal protein L27

60S ribosomal protein L27a

60S ribosomal protein L30

60S ribosomal protein L31

60S ribosomal protein L32

60S ribosomal protein L35a

60S ribosomal protein L34

60S ribosomal protein L35

60S ribosomal protein L36

60S ribosomal protein L37

60S ribosomal protein L38

60S ribosomal protein L39

60S ribosomal protein L37a

60S ribosomal protein L28

Large ribosomal subunit protein uL11

Eukaryotic translation initiation factor 6

Nucleolar GTP-binding protein 2

Guanine nucleotide-binding protein-like 3

GTP-binding protein 4

Protein LLP homolog

mRNA turnover protein 4 homolog

Notchless protein homolog 1

Ribosome biogenesis protein NSA2 homolog

Probable ribosome biogenesis protein RLP24

Ribosome production factor 2 homolog

Ribosome biogenesis regulatory protein homolog

Zinc finger protein 593

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