SMTL ID : 6sg9.1

Head domain of the mt-SSU assemblosome from Trypanosoma brucei

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-mer

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: UNK-f(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 18 residues within 4Å: Chain 8: Q.122, M.123, Q.124, T.125, D.126, L.140 Chain H: K.29, Y.30, N.31, S.32 Chain a: Q.173 Chain c: S.4, T.5, P.9, G.10 Chain f: X.2, X.3, X.4 14 PLIP interactions: 1 interactions with chain a, 3 interactions with chain c, 5 interactions with chain H, 5 interactions with chain 8 Hydrophobic interactions: a:Q.173, H:K.29, H:N.31, 8:L.140 Hydrogen bonds: c:S.4, c:S.4, c:P.9, H:K.29, H:N.31, H:N.31, 8:M.123, 8:Q.124, 8:T.125, 8:T.125

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

GTP.2: 24 residues within 4Å: Chain M: R.96, Q.99, T.100, G.108, F.109, L.110, P.150, T.151, G.152, C.153, G.154, K.155, S.156, A.157, Q.161, T.358, R.359, D.360, F.404, F.412, P.452, Q.453, V.456 Ligands: MG.3 21 PLIP interactions: 21 interactions with chain M Hydrogen bonds: M:R.96, M:R.96, M:Q.99, M:G.108, M:L.110, M:T.151, M:G.152, M:C.153, M:K.155, M:S.156, M:S.156, M:A.157, M:T.358, M:R.359, M:R.359, M:Q.453 Water bridges: M:G.95, M:S.156, M:S.156 Salt bridges: M:K.155, M:K.155

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain M: S.156, D.286, T.358 Ligands: GTP.2 4 PLIP interactions: 1 interactions with chain M, 3 Ligand-Water interactions Metal complexes: M:S.156, H2O.1, H2O.1, H2O.1

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain 2: C.591, C.597, C.614, C.837 3 PLIP interactions: 3 interactions with chain 2 Metal complexes: 2:C.591, 2:C.597, 2:C.614 ZN.7: 5 residues within 4Å: Chain 6: C.128, C.143, R.154, C.155, H.160 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:C.128, 6:C.143, 6:C.155, 6:H.160 ZN.8: 7 residues within 4Å: Ligands: ZN.9 Chain a: H.117, H.119, D.121, H.255, D.274, L.353 4 PLIP interactions: 4 interactions with chain a Metal complexes: a:H.117, a:H.119, a:H.255, a:D.274 ZN.9: 6 residues within 4Å: Ligands: ZN.8 Chain a: H.117, D.121, D.274, H.314, L.353 5 PLIP interactions: 5 interactions with chain a Metal complexes: a:D.121, a:D.274, a:D.274, a:H.314, a:L.353 ZN.10: 4 residues within 4Å: Chain c: C.59, C.62, C.85, H.94 4 PLIP interactions: 4 interactions with chain c Metal complexes: c:C.59, c:C.62, c:C.85, c:H.94

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.5: 16 residues within 4Å: Chain 2: Y.256, M.264, F.290, G.291, G.293, T.294, T.296, E.483, P.484, S.485, M.488, A.524, Y.525, E.529, I.530, E.534 6 PLIP interactions: 6 interactions with chain 2 Hydrogen bonds: 2:G.291, 2:G.293, 2:T.294, 2:T.294, 2:S.485, 2:E.534 SAH.6: 17 residues within 4Å: Chain 5: H.18, C.133, T.134, L.135, G.136, H.140, D.158, C.159, C.184, K.185, M.186, D.204, G.206, S.208, Q.211, F.233, E.332 11 PLIP interactions: 11 interactions with chain 5 Hydrogen bonds: 5:T.134, 5:T.134, 5:H.140, 5:C.159, 5:M.186, 5:S.208, 5:Q.211, 5:F.233, 5:E.332 Salt bridges: 5:H.18, 5:H.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saurer, M. et al., Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery. Science (2019)

Release Date

2019-09-18

Peptides

uS5m: A
uS11m: B
mS38: C
mt-SAF18: D
mt-SAF28: E
mt-SAF30: F
uS3m: H
uS9m: I
uS10m: J
uS14m: K
uS19m: L
mS29: M
mS33: N
mS35: O
mS49: P
mS50: Q
mS52: R
mS53: S
mS54: T
mS55 (KRIPP8): U
mS57: V
mS58: W
mS67: X
mS69: Y
mS70: Z
mS71: 0
mS72: 1
mt-SAF1 (RSM22): 2
mt-SAF4: 3
mt-SAF12 (KRIPP18): 4
mt-SAF14: 5
mt-SAF15: 6
mt-SAF16: 7
mt-SAF17: 8
mt-SAF19: 9
mt-SAF20: a
mt-SAF25: b
mt-SAF34: c
UNK-a: d
UNK-b: e
UNK-c: f
UNK-d: g
UNK-e: h
UNK-g: i
UNK-h: j
UNK-i: k
UNK-j: l
UNK-k: m
UNK-l: n
UNK-m: o
UNK-x: p

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
CE

B
CK

C
Cn

D
FJ

E
FY

F
Fa

H
CC

I
CI

J
CJ

K
CN

L
CS

M
Cg

N
Ci

O
Ck

P
DB

Q
DC

R
DE

S
DF

T
DG

U
DH

V
DJ

W
DK

X
DT

Y
DV

Z
DW

0
DX

1
DY

2
F1

3
F4

4
FD

5
FF

6
FG

7
FH

8
FI

9
FK

a
FL

b
FV

c
Fe

d
Ua

e
Ub

f
Uc

g
Ud

h
Ue

i
Ug

j
Uh

k
Ui

l
Uj

m
Uk

n
Ul

o
Um

p
Ux

uS5m

uS11m

mS38

mt-SAF18

mt-SAF28

mt-SAF30

uS3m

uS9m

uS10m

uS14m

uS19m

mS29

mS33

mS35

mS49

mS50

mS52

mS53

mS54

mS55 (KRIPP8)

mS57

mS58

mS67

mS69

mS70

mS71

mS72

mt-SAF1 (RSM22)

mt-SAF4

mt-SAF12 (KRIPP18)

mt-SAF14

mt-SAF15

mt-SAF16

mt-SAF17

mt-SAF19

mt-SAF20

mt-SAF25

mt-SAF34

UNK-a

UNK-b

UNK-c

UNK-d

UNK-e

UNK-g

UNK-h

UNK-i

UNK-j

UNK-k

UNK-l

UNK-m

UNK-x

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