- 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-mer
- Ligands
- 163 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 1 x SPM: SPERMINE(Non-covalent)
- 12 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)
K.162: 6 residues within 4Å:- Chain A: U.1633, G.1634, A.1635
- Chain U: Y.88, H.89, Q.90
No protein-ligand interaction detected (PLIP)K.163: 5 residues within 4Å:- Chain A: U.1633, A.1635, A.1636, G.1637, A.2039
No protein-ligand interaction detected (PLIP)K.164: 2 residues within 4Å:- Chain A: G.485, C.488
No protein-ligand interaction detected (PLIP)K.165: 1 residues within 4Å:- Chain A: G.830
No protein-ligand interaction detected (PLIP)K.166: 1 residues within 4Å:- Chain A: G.984
No protein-ligand interaction detected (PLIP)K.167: 3 residues within 4Å:- Chain A: G.2121, A.2122, G.2124
No protein-ligand interaction detected (PLIP)K.168: 5 residues within 4Å:- Chain A: C.2070, U.2073, G.2074, G.2133, U.2134
No protein-ligand interaction detected (PLIP)K.169: 7 residues within 4Å:- Chain A: C.2069, C.2070, G.2071, A.2072, U.2135, G.2139, A.2162
No protein-ligand interaction detected (PLIP)K.170: 3 residues within 4Å:- Chain A: C.2070, G.2071, G.2133
No protein-ligand interaction detected (PLIP)K.171: 6 residues within 4Å:- Chain A: U.2166, G.2168, C.2169, G.2199, U.2202, G.2203
No protein-ligand interaction detected (PLIP)K.172: 3 residues within 4Å:- Chain A: A.3300, U.3301, G.3325
No protein-ligand interaction detected (PLIP)K.173: 3 residues within 4Å:- Chain A: U.3345, C.3346
- Chain C: K.354
No protein-ligand interaction detected (PLIP)- 2 x ZN: ZINC ION(Non-covalent)
ZN.175: 6 residues within 4Å:- Chain Y: C.94, A.96, C.97, C.107, T.109, C.110
4 PLIP interactions:4 interactions with chain Y- Metal complexes: Y:C.94, Y:C.97, Y:C.107, Y:C.110
ZN.176: 5 residues within 4Å:- Chain 1: C.89, H.91, C.92, C.111, H.117
4 PLIP interactions:4 interactions with chain 1- Metal complexes: 1:C.89, 1:C.92, 1:C.111, 1:H.117
- 1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.177: 24 residues within 4Å:- Chain 3: W.287, F.290, R.291, Q.294, R.295, R.298, E.299
- Chain 7: R.102, E.108, Y.112
- Chain A: A.2755, G.2757, U.2759, U.2760
- Chain E: P.119, N.121, M.122, P.123, K.126, R.130, R.192, G.259, N.260
- Ligands: MG.178
18 PLIP interactions:10 interactions with chain 3, 2 interactions with chain 7, 6 interactions with chain E- Hydrogen bonds: 3:W.287, 3:R.291, 3:R.295, 3:E.299, 3:E.299, 7:E.108, 7:Y.112, E:K.126, E:N.260
- Salt bridges: 3:R.291, 3:R.291, 3:R.298, 3:R.298, E:K.126, E:R.130, E:R.130
- pi-Stacking: 3:W.287
- pi-Cation interactions: E:K.126
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Itoh, Y. et al., Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi. Nat Commun (2020)
- Release Date
- 2020-11-11
- Peptides
- 60S ribosomal protein L2: B
60S ribosomal protein L3: C
60S ribosomal protein L4, variant: D
50S ribosomal protein L5: E
60S ribosomal protein L6: F
RIBOSOMAL_L9 domain-containing protein: G
Uncharacterized protein: H
60S ribosomal protein L19: I
Ribosomal protein L13: J
50S ribosomal protein L14: K
Ribosomal protein L15: L
60S ribosomal protein L16: M
50S ribosomal protein L17: N
Mitochondrial ribosomal protein: O
Aconitate hydratase: P
Mitochondrial large ribosomal subunit: Q
Mitochondrial ribosomal protein subunit L23: R
KOW domain-containing protein: S
Uncharacterized protein: T
50S ribosomal protein L24: U
54S ribosomal protein L4, mitochondrial: V
50S ribosomal protein L30: W
Uncharacterized protein: X
Mitochondrial ribosomal protein subunit L32: Y
Uncharacterized protein: Z
Related to ribosomal protein L34, mitochondrial: 0
Ribosomal protein: 1
Mitochondrial large ribosomal subunit YmL35: 2
Uncharacterized protein: 3
Uncharacterized protein: 4
Mitochondrial ribosomal protein L43: 5
60S ribosomal protein L3: 6
50S ribosomal subunit L30: 7
Uncharacterized protein: 8
Uncharacterized protein: 9
Mitochondrial ribosomal protein L44: a
Uncharacterized protein: b
RNase III domain-containing protein: c
60S ribosomal protein L20: d
Mitoc_mL59 domain-containing protein: e
54S ribosomal protein L31, mitochondrial: f
Uncharacterized protein: g
60S ribosomal protein L1: h
L51_S25_CI-B8 domain-containing protein: i - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:B
BC
CD
DE
EF
FG
GH
fI
gJ
HK
IL
JM
KN
LO
MP
NQ
OR
PS
QT
RU
SV
TW
UX
VY
WZ
X0
Y1
02
13
24
35
46
57
68
79
8a
hb
ic
9d
ae
bf
cg
dh
ei
j
SMTL ID : 6yws.1
The structure of the large subunit of the mitoribosome from Neurospora crassa
60S ribosomal protein L2
60S ribosomal protein L3
60S ribosomal protein L4, variant
50S ribosomal protein L5
60S ribosomal protein L6
RIBOSOMAL_L9 domain-containing protein
Uncharacterized protein
60S ribosomal protein L19
Ribosomal protein L13
50S ribosomal protein L14
Ribosomal protein L15
60S ribosomal protein L16
50S ribosomal protein L17
Mitochondrial ribosomal protein
Aconitate hydratase
Mitochondrial large ribosomal subunit
Mitochondrial ribosomal protein subunit L23
KOW domain-containing protein
Uncharacterized protein
50S ribosomal protein L24
54S ribosomal protein L4, mitochondrial
50S ribosomal protein L30
Uncharacterized protein
Mitochondrial ribosomal protein subunit L32
Uncharacterized protein
Related to ribosomal protein L34, mitochondrial
Ribosomal protein
Mitochondrial large ribosomal subunit YmL35
Uncharacterized protein
Uncharacterized protein
Mitochondrial ribosomal protein L43
60S ribosomal protein L3
50S ribosomal subunit L30
Uncharacterized protein
Uncharacterized protein
Mitochondrial ribosomal protein L44
Uncharacterized protein
RNase III domain-containing protein
60S ribosomal protein L20
Mitoc_mL59 domain-containing protein
54S ribosomal protein L31, mitochondrial
Uncharacterized protein
60S ribosomal protein L1
L51_S25_CI-B8 domain-containing protein
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6yw5.1 | 6ywe.1 | 6ywe.2 | 6ywe.3 | 6ywe.4 | 6ywe.5 | 6ywe.6 | 6ywe.7 | 6ywe.8 | 6ywe.9 | 6ywe.10 | 6ywe.11 | 6ywe.12 | 6ywe.13 | 6ywe.14 | 6ywe.15 | 6ywe.16 | 6ywe.17 | 6ywe.18 | 6ywe.19 | 6ywe.20 | 6ywe.21 | 6ywe.22 | 6ywe.23 | 6ywe.24 | 6ywe.25 | 6ywe.26 | 6ywe.27 | 6ywe.28 | 6ywe.29 more...less...6ywe.30 | 6ywe.31 | 6ywe.32 | 6ywe.33 | 6ywe.34 | 6ywe.35 | 6ywe.36 | 6ywe.37 | 6ywe.38 | 6ywe.39 | 6ywe.40 | 6ywe.41 | 6ywe.42 | 6ywe.43 | 6ywe.44 | 6ywv.1 | 6ywx.1 | 6ywx.2 | 6ywx.3 | 6ywx.4 | 6ywx.5 | 6ywx.6 | 6ywx.7 | 6ywx.8 | 6ywx.9 | 6ywx.10 | 6ywx.11 | 6ywx.12 | 6ywx.13 | 6ywx.14 | 6ywx.15 | 6ywx.16 | 6ywx.17 | 6ywx.18 | 6ywx.19 | 6ywx.20 | 6ywx.21 | 6ywx.22 | 6ywx.23 | 6ywx.24 | 6ywx.25 | 6ywx.26 | 6ywx.27 | 6ywx.28 | 6ywx.29 | 6ywx.30 | 6ywx.31 | 6ywx.32 | 6ywx.33 | 6ywx.34 | 6ywx.35 | 6ywx.36 | 6ywx.37 | 6ywx.38 | 6ywx.39 | 6ywx.40 | 6ywx.41 | 6ywx.42 | 6ywx.79 | 6ywx.80 | 6ywy.1 | 6ywy.2 | 6ywy.3 | 6ywy.4 | 6ywy.5 | 6ywy.6 | 6ywy.7 | 6ywy.8 | 6ywy.9 | 6ywy.10 | 6ywy.11 | 6ywy.12 | 6ywy.13 | 6ywy.14 | 6ywy.15 | 6ywy.16 | 6ywy.17 | 6ywy.18 | 6ywy.19 | 6ywy.20 | 6ywy.21 | 6ywy.22 | 6ywy.23 | 6ywy.24 | 6ywy.25 | 6ywy.26 | 6ywy.27 | 6ywy.28 | 6ywy.29 | 6ywy.30 | 6ywy.31 | 6ywy.32 | 6ywy.33 | 6ywy.34 | 6ywy.35 | 6ywy.36 | 6ywy.37 | 6ywy.38 | 6ywy.39 | 6ywy.40 | 6ywy.41 | 6ywy.42 | 6ywy.79 | 6ywy.80