SMTL ID : 7aor.1

mt-SSU from Trypanosoma cruzi in complex with mt-IF-3.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

GTP.1: 21 residues within 4Å: Chain C: G.95, K.96, V.97, M.98, Q.99, L.100, M.101, R.107, G.108, F.109, L.110, K.151, C.153, G.154, K.155, S.156, A.157, T.358, D.360, Q.453 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:K.96, C:V.97, C:Q.99, C:Q.99, C:L.100, C:G.108, C:L.110, C:K.155, C:S.156, C:S.156, C:A.157, C:D.360, C:D.360, C:D.360 Salt bridges: C:K.151, C:K.151 pi-Cation interactions: C:F.109

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain C: G.95, S.156 Ligands: GTP.1 No protein-ligand interaction detected (PLIP)

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.3: 12 residues within 4Å: Chain M: K.205, R.209, E.234, R.236, I.240, K.283, L.284, R.285, I.286 Chain P: R.188 Chain t: U.3018, U.3020 14 PLIP interactions: 13 interactions with chain M, 1 interactions with chain P Hydrogen bonds: M:K.205, M:E.234, M:R.236, M:R.236, M:K.283, M:K.283, M:R.285, M:I.286, P:R.188 Salt bridges: M:K.205, M:R.209, M:R.236, M:R.285 pi-Cation interactions: M:R.236

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain 1: C.98, C.101, C.119, C.122 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.98, 1:C.101, 1:C.119, 1:C.122 ZN.5: 3 residues within 4Å: Chain 1: C.175, C.178, C.211 1 PLIP interactions: 1 interactions with chain 1 Metal complexes: 1:C.175 ZN.6: 4 residues within 4Å: Chain 9: H.63, C.67, M.70, C.93 3 PLIP interactions: 3 interactions with chain 9 Metal complexes: 9:H.63, 9:C.67, 9:C.93 ZN.7: 4 residues within 4Å: Chain p: C.341, C.344, C.354, H.373 4 PLIP interactions: 4 interactions with chain p Metal complexes: p:C.341, p:C.344, p:C.354, p:H.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soufari, H. et al., Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2021-04-28

Peptides

mS35: A
mS33: B
mS29: C
uS19: D
uS14m: E
uS10m: F
mS72: G
mS71: H
mS70: I
mS69: J
Rhodanese domain-containing protein: K
mS58: L
mS57: M
mS55: N
mS54: O
mS53: P
mS52: Q
mS50: R
mS49: S
mS51: T
bS18m: U
uS15m: V
uS11m: W
uS8m: X
uS9m: Y
mS73: Z
mS68: 0
mS66: 1
AKAP7_NLS domain-containing protein: 2
mS63: 3
mS62: 4
mS61: 5
mS56: 6
mS60: 7
mS47: 8
Sod_Fe_C domain-containing protein: 9
Superoxide dismutase, putative: a
Protein FYV4, mitochondrial: b
mS37: c
mS38: d
Trafficking protein particle complex subunit: e
mS59: f
mS26: g
mS23: h
mS22: i
bS21m: j
bS16m: k
bS6m: l
MURF5: m
Ribosomal_S5_C domain-containing protein: n
mt-iF3: o
mS48: p
30S Ribosomal protein S17-like protein: q
Ribosome protein S12: r
mS65: s

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
u

B
s

C
r

D
n

E
h

F
e

G
az

H
ay

I
ax

J
aw

K
au

L
ak

M
aj

N
ag

O
af

P
ae

Q
l

R
ac

S
ab

T
ad

U
m

V
i

W
f

X
c

Y
d

Z
ba

0
av

1
at

2
ar

3
aq

4
ap

5
ao

6
ai

7
an

8
z

9
y

a
x

b
w

c
v

d
bb

e
t

f
al

g
q

h
p

i
Ca

j
g

k
j

l
b

m
bd

n
a

o
bc

p
aa

q
k

r
be

s
as

mS35

mS33

mS29

uS19

uS14m

uS10m

mS72

mS71

mS70

mS69

Rhodanese domain-containing protein

mS58

mS57

mS55

mS54

mS53

mS52

mS50

mS49

mS51

bS18m

uS15m

uS11m

uS8m

uS9m

mS73

mS68

mS66

AKAP7_NLS domain-containing protein

mS63

mS62

mS61

mS56

mS60

mS47

Sod_Fe_C domain-containing protein

Superoxide dismutase, putative

Protein FYV4, mitochondrial

mS37

mS38

Trafficking protein particle complex subunit

mS59

mS26

mS23

mS22

bS21m

bS16m

bS6m

MURF5

Ribosomal_S5_C domain-containing protein

mt-iF3

mS48

30S Ribosomal protein S17-like protein

Ribosome protein S12

mS65