SMTL ID : 6hiz.1

Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the head of the small mitoribosomal subunit

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-mer

Ligands

2 x UNK- UNK- UNK- UNK- UNK: Unknown protein(Non-covalent)

UNK-UNK-UNK-UNK-UNK.1: 6 residues within 4Å: Chain D: E.244, T.464, Q.473 Chain K: H.94, R.95, Y.174 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: D:Q.473 Hydrogen bonds: D:E.244, D:E.244, K:Y.174, K:Y.174 UNK-UNK-UNK-UNK-UNK.2: 6 residues within 4Å: Chain C: V.743, V.754, L.755, T.756, V.757, S.758 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.743, C:V.754, C:L.755, C:T.756 Hydrogen bonds: C:V.754, C:T.756, C:T.756, C:S.758, C:S.758

2 x SPD: SPERMIDINE(Non-covalent)

SPD.3: 4 residues within 4Å: Chain B: H.267 Chain Z: U.398, A.399, A.459 No protein-ligand interaction detected (PLIP) SPD.9: 10 residues within 4Å: Chain B: R.292 Chain R: M.387 Chain Z: A.452, A.453, G.454, G.466, A.467, A.468, A.469, G.470 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain R Hydrogen bonds: B:R.292, R:M.387

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

UTP.4: 12 residues within 4Å: Chain F: R.188 Chain I: R.132, K.171, F.202, K.205, R.209, E.234, R.236, K.283, L.284, R.285 Chain Z: U.429 16 PLIP interactions: 15 interactions with chain I, 1 interactions with chain F Hydrogen bonds: I:K.205, I:R.209, I:E.234, I:R.236, I:R.285 Salt bridges: I:R.132, I:R.132, I:K.171, I:K.205, I:K.205, I:K.205, I:R.209, I:R.236, I:R.285, F:R.188 pi-Cation interactions: I:R.236

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

GTP.5: 23 residues within 4Å: Chain W: R.96, V.97, Q.99, T.100, G.108, F.109, L.110, R.112, T.151, G.152, C.153, G.154, K.155, S.156, A.157, T.357, T.358, R.359, D.360, F.412, P.452, Q.453 Ligands: MG.6 19 PLIP interactions: 19 interactions with chain W Hydrogen bonds: W:R.96, W:V.97, W:Q.99, W:T.100, W:G.108, W:L.110, W:G.152, W:K.155, W:S.156, W:S.156, W:S.156, W:A.157, W:T.358, W:R.359, W:D.360, W:D.360 Water bridges: W:G.95 Salt bridges: W:K.155, W:K.155

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

MG.6: 2 residues within 4Å: Chain W: S.156 Ligands: GTP.5 4 PLIP interactions: 1 interactions with chain W, 3 Ligand-Water interactions Metal complexes: W:S.156, H2O.1, H2O.1, H2O.1 MG.7: 1 residues within 4Å: Chain Z: U.415 No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramrath, D.J.F. et al., Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes. Science (2018)

Release Date

2018-09-26

Peptides

mS48: A
mS59: B
mS49: C
mS50: D
mS52: E
mS53: F
mS54: G
mS55: H
mS57: I
mS58: J
mS67: K
mS69: L
mS70: M
mS71: N
mS72: O
uS3m: P
uS9m: Q
uS10m: R
uS11m: S
uS14m: T
uS18m: U
uS19m: V
mS29: W
mS33: X
mS35: Y

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
DA

B
DL

C
DB

D
DC

E
DE

F
DF

G
DG

H
DH

I
DJ

J
DK

K
DT

L
DV

M
DW

N
DX

O
DY

P
CC

Q
CI

R
CJ

S
CK

T
CN

U
CR

V
CS

W
Cg

X
Ci

Y
Ck

mS48

mS59

mS49

mS50

mS52

mS53

mS54

mS55

mS57

mS58

mS67

mS69

mS70

mS71

mS72

uS3m

uS9m

uS10m

uS11m

uS14m

uS18m

uS19m

mS29

mS33

mS35

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