- 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-mer
- Ligands
- 49 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 13 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)
K.47: 5 residues within 4Å:- Chain A: C.152, A.153, C.157, C.158
- Ligands: MG.17
No protein-ligand interaction detected (PLIP)K.48: 6 residues within 4Å:- Chain A: C.187, A.189, U.190, A.191, U.202, A.204
No protein-ligand interaction detected (PLIP)K.49: 5 residues within 4Å:- Chain A: C.454, C.455, U.456, U.946, U.947
No protein-ligand interaction detected (PLIP)K.50: 6 residues within 4Å:- Chain A: A.612, C.616, G.617, C.618, G.682, U.683
No protein-ligand interaction detected (PLIP)K.51: 5 residues within 4Å:- Chain A: A.918, A.919, A.927, G.940
- Ligands: MG.28
No protein-ligand interaction detected (PLIP)K.52: 5 residues within 4Å:- Chain A: C.240, C.250, G.251
- Chain J: P.73, N.74
No protein-ligand interaction detected (PLIP)K.53: 5 residues within 4Å:- Chain A: C.920, A.921, A.922, G.923, A.926
No protein-ligand interaction detected (PLIP)K.54: 5 residues within 4Å:- Chain A: G.5, U.6, G.15, G.16, C.17
No protein-ligand interaction detected (PLIP)K.55: 2 residues within 4Å:- Chain A: C.258, G.259
No protein-ligand interaction detected (PLIP)K.56: 4 residues within 4Å:- Chain A: U.226, U.233, U.261, U.262
No protein-ligand interaction detected (PLIP)K.57: 4 residues within 4Å:- Chain A: U.555, G.556, U.713, G.714
No protein-ligand interaction detected (PLIP)K.58: 5 residues within 4Å:- Chain A: A.918, A.919, C.920, G.923, G.924
No protein-ligand interaction detected (PLIP)K.59: 3 residues within 4Å:- Chain A: U.238, C.254, A.255
No protein-ligand interaction detected (PLIP)- 1 x ZN: ZINC ION(Non-covalent)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.62: 10 residues within 4Å:- Chain E: C.105, G.107, I.108
- Chain P: K.65, C.66, C.69, E.70, C.101, K.103, K.104
4 PLIP interactions:1 interactions with chain E, 3 interactions with chain P,- Metal complexes: E:C.105, P:C.66, P:C.69, P:C.101
FES.63: 7 residues within 4Å:- Chain M: G.25, C.26, R.29
- Chain T: C.139, C.141, C.149, P.150
4 PLIP interactions:3 interactions with chain T, 1 interactions with chain M,- Metal complexes: T:C.139, T:C.141, T:C.149, M:C.26
- 1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.64: 25 residues within 4Å:- Chain X: H.60, P.77, R.79, Y.80, Q.83, C.91, L.92, M.93, R.95, E.122, K.123, G.124, T.125, G.126, K.127, T.128, L.129, S.304, T.306, Y.341, Y.353, P.381, E.382, E.385
- Ligands: MG.65
20 PLIP interactions:20 interactions with chain X- Hydrogen bonds: X:Q.83, X:M.93, X:M.93, X:R.95, X:E.122, X:G.124, X:T.125, X:G.126, X:K.127, X:T.128, X:T.128, X:L.129, X:T.306, X:T.306, X:T.306, X:Y.341
- Water bridges: X:K.127, X:S.302
- Salt bridges: X:K.127, X:K.127
- 1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)
SAH.67: 27 residues within 4Å:- Chain 5: D.94, M.95, T.96, F.97, G.98, S.99, G.100, G.101, H.102, L.118, D.119, R.120, D.121, A.124, G.144, Q.145, F.146, D.169, L.170, G.171, C.172, S.173, S.174, Q.176, M.196, E.295, E.298
13 PLIP interactions:13 interactions with chain 5- Hydrogen bonds: 5:S.99, 5:G.100, 5:G.101, 5:H.102, 5:H.102, 5:R.120, 5:R.120, 5:F.146, 5:D.169, 5:S.173, 5:Q.176, 5:E.298
- pi-Stacking: 5:F.146
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Itoh, Y. et al., Mechanism of mitoribosomal small subunit biogenesis and preinitiation. Nature (2022)
- Release Date
- 2022-06-15
- Peptides
- 28S ribosomal protein S2, mitochondrial: B
28S ribosomal protein S24, mitochondrial: C
28S ribosomal protein S5, mitochondrial: D
28S ribosomal protein S6, mitochondrial: E
28S ribosomal protein S7, mitochondrial: F
28S ribosomal protein S9, mitochondrial: G
28S ribosomal protein S10, mitochondrial: H
28S ribosomal protein S11, mitochondrial: I
28S ribosomal protein S12, mitochondrial: J
28S ribosomal protein S14, mitochondrial: K
28S ribosomal protein S15, mitochondrial: L
28S ribosomal protein S16, mitochondrial: M
28S ribosomal protein S17, mitochondrial: N
28S ribosomal protein S18b, mitochondrial: O
28S ribosomal protein S18c, mitochondrial: P
28S ribosomal protein S21, mitochondrial: Q
28S ribosomal protein S22, mitochondrial: R
28S ribosomal protein S23, mitochondrial: S
28S ribosomal protein S25, mitochondrial: T
28S ribosomal protein S26, mitochondrial: U
28S ribosomal protein S27, mitochondrial: V
28S ribosomal protein S28, mitochondrial: W
28S ribosomal protein S29, mitochondrial: X
28S ribosomal protein S31, mitochondrial: Y
28S ribosomal protein S33, mitochondrial: Z
28S ribosomal protein S34, mitochondrial: 0
28S ribosomal protein S35, mitochondrial: 1
Aurora kinase A-interacting protein: 2
Pentatricopeptide repeat domain-containing protein 3, mitochondrial: 3
Putative ribosome-binding factor A, mitochondrial: 4
12S rRNA N4-methylcytidine methyltransferase: 5 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:B
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
LM
MN
NO
OP
PQ
QR
RS
ST
TU
UV
VW
WX
XY
YZ
Z0
01
12
33
44
a5
b
- 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-mer
- Ligands
- 49 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 13 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)
- 1 x ZN: ZINC ION(Non-covalent)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Itoh, Y. et al., Mechanism of mitoribosomal small subunit biogenesis and preinitiation. Nature (2022)
- Release Date
- 2022-06-15
- Peptides
- 28S ribosomal protein S2, mitochondrial: B
28S ribosomal protein S24, mitochondrial: C
28S ribosomal protein S5, mitochondrial: D
28S ribosomal protein S6, mitochondrial: E
28S ribosomal protein S7, mitochondrial: F
28S ribosomal protein S9, mitochondrial: G
28S ribosomal protein S10, mitochondrial: H
28S ribosomal protein S11, mitochondrial: I
28S ribosomal protein S12, mitochondrial: J
28S ribosomal protein S14, mitochondrial: K
28S ribosomal protein S15, mitochondrial: L
28S ribosomal protein S16, mitochondrial: M
28S ribosomal protein S17, mitochondrial: N
28S ribosomal protein S18b, mitochondrial: O
28S ribosomal protein S18c, mitochondrial: P
28S ribosomal protein S21, mitochondrial: Q
28S ribosomal protein S22, mitochondrial: R
28S ribosomal protein S23, mitochondrial: S
28S ribosomal protein S25, mitochondrial: T
28S ribosomal protein S26, mitochondrial: U
28S ribosomal protein S27, mitochondrial: V
28S ribosomal protein S28, mitochondrial: W
28S ribosomal protein S29, mitochondrial: X
28S ribosomal protein S31, mitochondrial: Y
28S ribosomal protein S33, mitochondrial: Z
28S ribosomal protein S34, mitochondrial: 0
28S ribosomal protein S35, mitochondrial: 1
Aurora kinase A-interacting protein: 2
Pentatricopeptide repeat domain-containing protein 3, mitochondrial: 3
Putative ribosome-binding factor A, mitochondrial: 4
12S rRNA N4-methylcytidine methyltransferase: 5 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:B
BC
CD
DE
EF
FG
GH
HI
IJ
JK
KL
LM
MN
NO
OP
PQ
QR
RS
ST
TU
UV
VW
WX
XY
YZ
Z0
01
12
33
44
a5
b