- 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-mer
- Ligands
- 144 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.107: 22 residues within 4Å:- Chain 2: W.287, F.290, R.291, Q.294, R.295, R.298, E.299
- Chain 6: R.102, E.108, Y.112
- Chain A: A.2755, G.2757, U.2758, U.2759, U.2760
- Chain E: P.119, N.121, M.122, K.126, R.130, G.259, N.260
15 PLIP interactions:5 interactions with chain E, 8 interactions with chain 2, 2 interactions with chain 6- Hydrogen bonds: E:K.126, E:N.260, 2:R.291, 6:E.108, 6:Y.112
- Salt bridges: E:K.126, E:R.130, 2:R.291, 2:R.291, 2:R.295, 2:R.298, 2:R.298
- pi-Cation interactions: E:K.126, 2:R.295
- pi-Stacking: 2:W.287
- 1 x SPM: SPERMINE(Non-covalent)
- 23 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)
K.145: 2 residues within 4Å:- Chain A: U.603, G.991
Ligand excluded by PLIPK.146: 3 residues within 4Å:- Chain A: A.367, A.368, U.369
Ligand excluded by PLIPK.147: 4 residues within 4Å:- Chain A: C.68, A.552, A.553, A.554
Ligand excluded by PLIPK.148: 1 residues within 4Å:- Chain A: U.2286
Ligand excluded by PLIPK.149: 3 residues within 4Å:- Chain A: G.969, A.3040, U.3041
Ligand excluded by PLIPK.150: 3 residues within 4Å:- Chain A: A.2469, A.2470, G.2471
Ligand excluded by PLIPK.151: 3 residues within 4Å:- Chain A: G.1001, G.1457, G.1458
Ligand excluded by PLIPK.152: 5 residues within 4Å:- Chain A: U.2286, A.2287, G.2288, A.3029, A.3066
Ligand excluded by PLIPK.153: 3 residues within 4Å:- Chain A: C.916, G.917, A.945
Ligand excluded by PLIPK.154: 3 residues within 4Å:- Chain A: A.1894, U.1895
- Chain C: H.247
Ligand excluded by PLIPK.155: 4 residues within 4Å:- Chain A: U.2309, U.2310, G.2440, A.2441
Ligand excluded by PLIPK.156: 6 residues within 4Å:- Chain A: A.2018, A.2019, U.2059, G.2060
- Chain B: T.316, R.318
Ligand excluded by PLIPK.157: 4 residues within 4Å:- Chain A: A.970, C.971, C.976, U.977
Ligand excluded by PLIPK.158: 3 residues within 4Å:- Chain A: G.2056
- Chain B: H.117, T.316
Ligand excluded by PLIPK.159: 3 residues within 4Å:- Chain A: A.415, G.416, U.417
Ligand excluded by PLIPK.160: 2 residues within 4Å:- Chain A: A.465, G.466
Ligand excluded by PLIPK.161: 3 residues within 4Å:- Chain A: C.522, G.524, A.527
Ligand excluded by PLIPK.162: 6 residues within 4Å:- Chain A: G.2640, U.2641, A.2642, U.2790, G.2791, C.2792
Ligand excluded by PLIPK.163: 4 residues within 4Å:- Chain A: A.866, C.1462, A.1463
- Chain K: K.66
Ligand excluded by PLIPK.164: 5 residues within 4Å:- Chain A: U.1633, A.1635, A.1636, G.1637, A.2039
Ligand excluded by PLIPK.165: 7 residues within 4Å:- Chain A: A.622, G.623, U.994, U.1522, G.1523, A.1524
- Chain K: R.68
Ligand excluded by PLIPK.166: 5 residues within 4Å:- Chain 0: K.98, Y.108
- Chain A: G.3304, U.3305, A.3317
Ligand excluded by PLIPK.167: 3 residues within 4Å:- Chain A: A.2768, A.2769, A.2770
Ligand excluded by PLIP- 2 x ZN: ZINC ION(Non-covalent)
ZN.169: 5 residues within 4Å:- Chain X: C.94, A.96, C.97, C.107, C.110
3 PLIP interactions:3 interactions with chain X- Metal complexes: X:C.94, X:C.97, X:C.110
ZN.170: 5 residues within 4Å:- Chain 0: C.89, H.91, C.92, C.111, H.117
4 PLIP interactions:4 interactions with chain 0- Metal complexes: 0:C.89, 0:C.92, 0:C.111, 0:H.117
- 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
Uncharacterized protein: G
60S ribosomal protein L19: H
Ribosomal protein L13: I
50S ribosomal protein L14: J
50S ribosomal subunit protein L15: K
60S ribosomal protein L16: L
50S ribosomal protein L17: M
Mitochondrial ribosomal protein: N
Aconitate hydratase: O
Mitochondrial large ribosomal subunit: P
Mitochondrial ribosomal protein subunit L23: Q
KOW domain-containing protein: R
Uncharacterized protein: S
50S ribosomal protein L24: T
54S ribosomal protein L4, mitochondrial: U
50S ribosomal protein L30: V
Uncharacterized protein: W
Mitochondrial ribosomal protein subunit L32: X
Uncharacterized protein: Y
Uncharacterized protein: Z
Ribosomal protein: 0
Mitochondrial large ribosomal subunit YmL35: 1
Uncharacterized protein: 2
Uncharacterized protein: 3
Mitochondrial ribosomal protein L43: 4
60S ribosomal protein L3: 5
50S ribosomal subunit L30: 6
Uncharacterized protein: 7
Uncharacterized protein: 8
Mitochondrial ribosomal protein L44: 9
Uncharacterized protein: a
RNase III domain-containing protein: b
60S ribosomal protein L20: c
Mitochondrial 60S ribosomal protein L25: d
54S ribosomal protein L31, mitochondrial: e
Uncharacterized protein: f
ATPase synthesis protein 25, mitochondrial: g - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:B
BC
CD
DE
EF
FG
fH
gI
HJ
IK
JL
KM
LN
MO
NP
OQ
PR
QS
RT
SU
TV
UW
VX
WY
XZ
Y0
01
12
23
34
45
56
67
78
89
ha
ib
9c
ad
be
cf
dg
n
SMTL ID : 6ywv.1
The structure of the Atp25 bound assembly intermediate 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
Uncharacterized protein
60S ribosomal protein L19
Ribosomal protein L13
50S ribosomal protein L14
50S ribosomal subunit 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
Uncharacterized protein
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
Mitochondrial 60S ribosomal protein L25
54S ribosomal protein L31, mitochondrial
Uncharacterized protein
ATPase synthesis protein 25, mitochondrial
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6yw5.1 | 6ywe.2 | 6ywe.3 | 6ywe.4 | 6ywe.5 | 6ywe.6 | 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 | 6ywe.30 | 6ywe.31 more...less...6ywe.32 | 6ywe.33 | 6ywe.34 | 6ywe.35 | 6ywe.36 | 6ywe.37 | 6ywe.38 | 6ywe.39 | 6ywe.40 | 6ywe.41 | 6ywe.42 | 6ywe.43 | 6yws.1 | 6ywx.1 | 6ywx.2 | 6ywx.3 | 6ywx.4 | 6ywx.5 | 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 | 6ywy.1 | 6ywy.2 | 6ywy.3 | 6ywy.4 | 6ywy.5 | 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