- 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-mer
- Ligands
- 49 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.2: 13 residues within 4Å:- Chain D: A.134, A.135, A.136, U.301, A.399, A.400, C.401
- Chain K: R.38
- Chain M: L.194, Y.195, Y.196, R.197
- Ligands: MG.27
3 PLIP interactions:1 interactions with chain K, 2 interactions with chain M- Salt bridges: K:R.38
- Hydrophobic interactions: M:Y.195
- Hydrogen bonds: M:Y.196
- 1 x SPM: SPERMINE(Non-functional Binders)
- 1 x SRY: STREPTOMYCIN(Non-covalent)
- 17 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)
K.50: 3 residues within 4Å:- Chain D: C.55, C.60, C.195
Ligand excluded by PLIPK.51: 4 residues within 4Å:- Chain D: G.70, A.71, G.72, G.144
Ligand excluded by PLIPK.52: 5 residues within 4Å:- Chain D: C.243, C.253, G.254
- Chain K: P.73, N.74
Ligand excluded by PLIPK.53: 5 residues within 4Å:- Chain D: C.458, U.460, U.945, U.946, G.947
Ligand excluded by PLIPK.54: 3 residues within 4Å:- Chain D: G.552, G.553, G.774
Ligand excluded by PLIPK.55: 4 residues within 4Å:- Chain D: A.551, G.552, G.714, G.715
Ligand excluded by PLIPK.56: 3 residues within 4Å:- Chain D: G.552, G.553, A.554
Ligand excluded by PLIPK.57: 6 residues within 4Å:- Chain D: A.609, U.610, C.683, U.688, G.689, U.690
Ligand excluded by PLIPK.58: 3 residues within 4Å:- Chain D: C.615, G.681, U.682
Ligand excluded by PLIPK.59: 3 residues within 4Å:- Chain D: C.683, G.687, U.688
Ligand excluded by PLIPK.60: 3 residues within 4Å:- Chain D: A.718, G.742, A.743
Ligand excluded by PLIPK.61: 4 residues within 4Å:- Chain D: G.528, G.529, G.829, U.830
Ligand excluded by PLIPK.62: 4 residues within 4Å:- Chain D: A.917, A.918, A.926, G.939
Ligand excluded by PLIPK.63: 5 residues within 4Å:- Chain D: G.842, U.843, C.844, G.912, U.913
Ligand excluded by PLIPK.64: 5 residues within 4Å:- Chain D: C.153, A.154, C.157, C.158, C.159
Ligand excluded by PLIPK.65: 4 residues within 4Å:- Chain D: C.188, U.191, A.192, U.203
Ligand excluded by PLIPK.66: 3 residues within 4Å:- Chain D: G.240, U.241, A.258
Ligand excluded by PLIP- 1 x ZN: ZINC ION(Non-covalent)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.70: 4 residues within 4Å:- Chain G: C.105
- Chain Q: C.65, C.68, C.100
4 PLIP interactions:3 interactions with chain Q, 1 interactions with chain G,- Metal complexes: Q:C.65, Q:C.68, Q:C.100, G:C.105
FES.71: 5 residues within 4Å:- Chain N: C.26, R.29
- Chain U: C.139, C.141, C.149
4 PLIP interactions:3 interactions with chain U, 1 interactions with chain N,- Metal complexes: U:C.139, U:C.141, U:C.149, N:C.26
- 1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.73: 18 residues within 4Å:- Chain X: P.84, L.99, M.100, R.102, K.130, G.131, T.132, G.133, K.134, T.135, L.136, S.311, T.313, Y.348, P.388, S.389, E.392
- Ligands: MG.72
13 PLIP interactions:13 interactions with chain X- Hydrogen bonds: X:Q.90, X:M.100, X:M.100, X:G.131, X:T.132, X:G.133, X:K.134, X:T.135, X:L.136, X:T.313, X:T.313
- Salt bridges: X:K.134, X:K.134
- 1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)
GNP.74: 11 residues within 4Å:- Chain X: Y.173, R.177, Y.208, V.209, D.238, G.241, I.242, K.245, H.291, N.292, K.295
13 PLIP interactions:13 interactions with chain X- Hydrogen bonds: X:Y.173, X:R.177, X:R.177, X:V.209, X:V.209, X:V.209, X:D.238, X:H.291, X:N.292, X:K.295
- Salt bridges: X:D.238, X:K.245, X:K.295
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Cipullo, M. et al., GTPBP8 plays a role in mitoribosome formation in human mitochondria. Nat Commun (2024)
- Release Date
- 2024-06-26
- Peptides
- 28S ribosomal protein S34, mitochondrial: A
28S ribosomal protein S35, mitochondrial: B
Aurora kinase A-interacting protein: C
28S ribosomal protein S2, mitochondrial: E
28S ribosomal protein S24, mitochondrial: F
28S ribosomal protein S6, mitochondrial: G
28S ribosomal protein S7, mitochondrial: H
28S ribosomal protein S10, mitochondrial: I
28S ribosomal protein S11, mitochondrial: J
28S ribosomal protein S12, mitochondrial: K
28S ribosomal protein S14, mitochondrial: L
28S ribosomal protein S15, mitochondrial: M
28S ribosomal protein S16, mitochondrial: N
28S ribosomal protein S17, mitochondrial: O
28S ribosomal protein S18b, mitochondrial: P
28S ribosomal protein S18c, mitochondrial: Q
28S ribosomal protein S21, mitochondrial: R
28S ribosomal protein S22, mitochondrial: S
28S ribosomal protein S23, mitochondrial: T
28S ribosomal protein S25, mitochondrial: U
28S ribosomal protein S26, 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 S5, mitochondrial: 0
28S ribosomal protein S9, mitochondrial: 1
28S ribosomal protein S27, mitochondrial: 2
Pentatricopeptide repeat domain-containing protein 3, mitochondrial: 3 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
0B
1C
3E
BF
CG
EH
FI
HJ
IK
JL
KM
LN
MO
NP
OQ
PR
QS
RT
SU
TV
UW
WX
XY
YZ
Z0
D1
G2
V3
4
SMTL ID : 8qrk.1
mt-SSU assembly intermediate in GTPBP8 knock-out cells, state 1
28S ribosomal protein S34, mitochondrial
28S ribosomal protein S35, mitochondrial
Aurora kinase A-interacting protein
28S ribosomal protein S2, mitochondrial
28S ribosomal protein S24, mitochondrial
28S ribosomal protein S6, mitochondrial
28S ribosomal protein S7, mitochondrial
28S ribosomal protein S10, mitochondrial
28S ribosomal protein S11, mitochondrial
28S ribosomal protein S12, mitochondrial
28S ribosomal protein S14, mitochondrial
28S ribosomal protein S15, mitochondrial
28S ribosomal protein S16, mitochondrial
28S ribosomal protein S17, mitochondrial
28S ribosomal protein S18b, mitochondrial
28S ribosomal protein S18c, mitochondrial
28S ribosomal protein S21, mitochondrial
28S ribosomal protein S22, mitochondrial
28S ribosomal protein S23, mitochondrial
28S ribosomal protein S25, mitochondrial
28S ribosomal protein S26, mitochondrial
28S ribosomal protein S28, mitochondrial
28S ribosomal protein S29, mitochondrial
28S ribosomal protein S31, mitochondrial
28S ribosomal protein S33, mitochondrial
28S ribosomal protein S5, mitochondrial
28S ribosomal protein S9, mitochondrial
28S ribosomal protein S27, mitochondrial
Pentatricopeptide repeat domain-containing protein 3, mitochondrial
Related Entries With Identical Sequence
3j9m.52 | 3j9m.53 | 3j9m.54 | 3j9m.55 | 3j9m.56 | 3j9m.57 | 3j9m.58 | 3j9m.59 | 3j9m.60 | 3j9m.61 | 3j9m.62 | 3j9m.63 | 3j9m.64 | 3j9m.65 | 3j9m.66 | 3j9m.68 | 3j9m.69 | 3j9m.70 | 3j9m.71 | 3j9m.72 | 3j9m.73 | 3j9m.74 | 3j9m.75 | 3j9m.76 | 3j9m.77 | 3j9m.78 | 3j9m.80 | 6rw4.1 | 6rw5.1 | 6vlz.1 more...less...6vlz.2 | 6vlz.3 | 6vlz.4 | 6vlz.5 | 6vlz.6 | 6vlz.7 | 6vlz.8 | 6vlz.9 | 6vlz.10 | 6vlz.12 | 6vlz.13 | 6vlz.14 | 6vlz.16 | 6vlz.17 | 6vlz.18 | 6vlz.19 | 6vlz.20 | 6vlz.21 | 6vlz.22 | 6vlz.23 | 6vlz.24 | 6vlz.25 | 6vlz.26 | 6vlz.27 | 6vlz.28 | 6vlz.29 | 6vlz.30 | 6zm5.57 | 6zm5.58 | 6zm5.59 | 6zm5.60 | 6zm5.61 | 6zm5.62 | 6zm5.63 | 6zm5.65 | 6zm5.66 | 6zm5.67 | 6zm5.68 | 6zm5.69 | 6zm5.70 | 6zm5.71 | 6zm5.72 | 6zm5.73 | 6zm5.74 | 6zm5.75 | 6zm5.76 | 6zm5.77 | 6zm5.78 | 6zm5.79 | 6zm5.80 | 6zm5.81 | 6zm5.82 | 6zm5.83 | 6zm5.85 | 6zm5.86 | 6zm6.57 | 6zm6.58 | 6zm6.59 | 6zm6.60 | 6zm6.61 | 6zm6.62 | 6zm6.63 | 6zm6.65 | 6zm6.66 | 6zm6.67 | 6zm6.68 | 6zm6.69 | 6zm6.70 | 6zm6.71 | 6zm6.72 | 6zm6.73 | 6zm6.74 | 6zm6.75 | 6zm6.76 | 6zm6.77 | 6zm6.78 | 6zm6.79 | 6zm6.80 | 6zm6.81 | 6zm6.82 | 6zm6.83 | 6zm6.85 | 6zm6.86 | 6zs9.11 | 6zs9.12 | 6zs9.14 | 6zs9.17 | 6zs9.18 | 6zs9.19 | 6zs9.20 | 6zs9.21 | 6zs9.22 | 6zs9.23 | 6zs9.24 | 6zs9.25 | 6zs9.26 | 6zs9.27 | 6zs9.28 | 6zs9.29 | 6zs9.30 | 6zs9.31 | 6zs9.32 | 6zs9.33 | 6zs9.34 | 6zs9.35 | 6zs9.36 | 6zs9.37 | 6zs9.38 | 6zs9.40 | 6zs9.41 | 6zsa.11 | 6zsa.12 | 6zsa.14 | 6zsa.15 | 6zsa.16 | 6zsa.17 | 6zsa.18 | 6zsa.19 | 6zsa.20 | 6zsa.21 | 6zsa.22 | 6zsa.23 | 6zsa.24 | 6zsa.25 | 6zsa.26 | 6zsa.27 | 6zsa.28 | 6zsa.29 | 6zsa.30 | 6zsa.32 | 6zsa.33 | 6zsa.34 | 6zsa.35 | 6zsa.36 | 6zsa.37 | 6zsa.38 | 6zsa.39 | 6zsa.40 | 6zsb.11 | 6zsb.12 | 6zsb.14 | 6zsb.15 | 6zsb.16 | 6zsb.17 | 6zsb.18 | 6zsb.19 | 6zsb.20 | 6zsb.21 | 6zsb.22 | 6zsb.23 | 6zsb.24 | 6zsb.25 | 6zsb.26 | 6zsb.27 | 6zsb.28 | 6zsb.29 | 6zsb.30 | 6zsb.32 | 6zsb.33 | 6zsb.34 | 6zsb.35 | 6zsb.36 | 6zsb.37 | 6zsb.38 | 6zsb.39 | 6zsb.40 | 6zsc.11 | 6zsc.12 | 6zsc.14 | 6zsc.15 | 6zsc.16 | 6zsc.17 | 6zsc.18 | 6zsc.19 | 6zsc.20 | 6zsc.21 | 6zsc.22 | 6zsc.23 | 6zsc.24 | 6zsc.25 | 6zsc.26 | 6zsc.27 | 6zsc.28 | 6zsc.29 | 6zsc.30 | 6zsc.32 | 6zsc.33 | 6zsc.34 | 6zsc.35 | 6zsc.36 | 6zsc.37 | 6zsc.38 | 6zsc.39 | 6zsc.40 | 6zsd.11 | 6zsd.12 | 6zsd.14 | 6zsd.15 | 6zsd.16 | 6zsd.17 | 6zsd.18 | 6zsd.19 | 6zsd.20 | 6zsd.21 | 6zsd.22 | 6zsd.23 | 6zsd.24 | 6zsd.25 | 6zsd.26 | 6zsd.27 | 6zsd.28 | 6zsd.29 | 6zsd.30 | 6zsd.32 | 6zsd.33 | 6zsd.34 | 6zsd.35 | 6zsd.36 | 6zsd.37 | 6zsd.38 | 6zsd.39 | 6zsd.40 | 6zse.11 | 6zse.12 | 6zse.14 | 6zse.15 | 6zse.16 | 6zse.17 | 6zse.18 | 6zse.19 | 6zse.20 | 6zse.21 | 6zse.22 | 6zse.23 | 6zse.24 | 6zse.25 | 6zse.26 | 6zse.27 | 6zse.28 | 6zse.29 | 6zse.30 | 6zse.32 | 6zse.33 | 6zse.34 | 6zse.35 | 6zse.36 | 6zse.37 | 6zse.38 | 6zse.39 | 6zse.40 | 6zsg.11 | 6zsg.12 | 6zsg.14 | 6zsg.15 | 6zsg.16 | 6zsg.17 | 6zsg.18 | 6zsg.19 | 6zsg.20 | 6zsg.21 | 6zsg.22 | 6zsg.23 | 6zsg.24 | 6zsg.25 | 6zsg.26 | 6zsg.27 | 6zsg.28 | 6zsg.29 | 6zsg.30 | 6zsg.31 | 6zsg.32 | 6zsg.33 | 6zsg.34 | 6zsg.35 | 6zsg.36 | 6zsg.37 | 6zsg.38 | 6zsg.39 | 6zsg.40 | 7a5k.53 | 7a5k.54 | 7a5k.55 | 7a5k.56 | 7a5k.57 | 7a5k.58 | 7a5k.59 | 7a5k.60 | 7a5k.61 | 7a5k.62 | 7a5k.63 | 7a5k.64 | 7a5k.65 | 7a5k.66 | 7a5k.67 | 7a5k.69 | 7a5k.70 | 7a5k.71 | 7a5k.72 | 7a5k.73 | 7a5k.74 | 7a5k.75 | 7a5k.76 | 7a5k.77 | 7a5k.78 | 7a5k.79 | 7a5k.81 | 7a5k.82 | 7og4.11 | 7og4.12 | 7og4.14 | 7og4.15 | 7og4.16 | 7og4.17 | 7og4.18 | 7og4.19 | 7og4.20 | 7og4.21 | 7og4.22 | 7og4.23 | 7og4.24 | 7og4.25 | 7og4.26 | 7og4.27 | 7og4.28 | 7og4.29 | 7og4.30 | 7og4.32 | 7og4.33 | 7og4.34 | 7og4.35 | 7og4.36 | 7og4.37 | 7og4.38 | 7og4.39 | 7og4.40 | 7p2e.1 | 7pnx.1 | 7pny.1 | 7pnz.1 | 7po0.1 | 7po1.1 | 7po2.1 | 7po3.1 | 7qi4.1 | 7qi4.2 | 7qi4.3 | 7qi4.4 | 7qi4.5 | 7qi4.6 | 7qi4.7 | 7qi4.9 | 7qi4.10 | 7qi4.11 | 7qi4.12 | 7qi4.13 | 7qi4.14 | 7qi4.15 | 7qi4.17 | 7qi4.18 | 7qi4.19 | 7qi4.20 | 7qi4.21 | 7qi4.22 | 7qi4.23 | 7qi4.24 | 7qi4.25 | 7qi4.27 | 7qi4.29 | 7qi4.30 | 7qi5.1 | 7qi5.2 | 7qi5.3 | 7qi5.4 | 7qi5.5 | 7qi5.6 | 7qi5.7 | 7qi5.9 | 7qi5.10 | 7qi5.11 | 7qi5.12 | 7qi5.13 | 7qi5.14 | 7qi5.15 | 7qi5.17 | 7qi5.18 | 7qi5.19 | 7qi5.20 | 7qi5.21 | 7qi5.22 | 7qi5.23 | 7qi5.24 | 7qi5.25 | 7qi5.27 | 7qi5.29 | 7qi5.30 | 7qi6.1 | 7qi6.2 | 7qi6.3 | 7qi6.4 | 7qi6.5 | 7qi6.6 | 7qi6.7 | 7qi6.9 | 7qi6.10 | 7qi6.11 | 7qi6.12 | 7qi6.13 | 7qi6.14 | 7qi6.15 | 7qi6.17 | 7qi6.18 | 7qi6.19 | 7qi6.20 | 7qi6.21 | 7qi6.22 | 7qi6.23 | 7qi6.24 | 7qi6.25 | 7qi6.27 | 7qi6.29 | 7qi6.30 | 8any.1 | 8any.2 | 8any.3 | 8any.4 | 8any.5 | 8any.6 | 8any.7 | 8any.9 | 8any.10 | 8any.11 | 8any.12 | 8any.13 | 8any.14 | 8any.15 | 8any.17 | 8any.18 | 8any.19 | 8any.20 | 8any.21 | 8any.22 | 8any.23 | 8any.24 | 8any.26 | 8any.28 | 8any.86 | 8any.88 | 8csp.1 | 8csq.1 | 8csr.1 | 8css.1 | 8cst.1 | 8csu.1 | 8k2a.51 | 8k2a.52 | 8k2a.53 | 8k2a.54 | 8k2a.55 | 8k2a.56 | 8k2a.57 | 8k2a.58 | 8k2a.59 | 8k2a.60 | 8k2a.61 | 8k2a.62 | 8k2a.63 | 8k2a.64 | 8k2a.65 | 8k2a.67 | 8k2a.68 | 8k2a.69 | 8k2a.70 | 8k2a.71 | 8k2a.72 | 8k2a.73 | 8k2a.74 | 8k2a.75 | 8k2a.76 | 8k2a.77 | 8k2a.79 | 8k2a.80 | 8oir.58 | 8oir.59 | 8oir.60 | 8oir.61 | 8oir.62 | 8oir.63 | 8oir.64 | 8oir.65 | 8oir.66 | 8oir.67 | 8oir.68 | 8oir.69 | 8oir.70 | 8oir.72 | 8oir.73 | 8oir.74 | 8oir.75 | 8oir.76 | 8oir.77 | 8oir.78 | 8oir.79 | 8oir.80 | 8oir.82 | 8oir.84 | 8oir.85 | 8oir.86 | 8oir.88 | 8ois.1 | 8qrl.1 | 8qrm.1 | 8qrn.1 | 8xt2.51 | 8xt2.52 | 8xt2.53 | 8xt2.54 | 8xt2.55 | 8xt2.56 | 8xt2.57 | 8xt2.58 | 8xt2.59 | 8xt2.60 | 8xt2.61 | 8xt2.62 | 8xt2.63 | 8xt2.64 | 8xt2.65 | 8xt2.67 | 8xt2.68 | 8xt2.69 | 8xt2.70 | 8xt2.71 | 8xt2.72 | 8xt2.73 | 8xt2.74 | 8xt2.75 | 8xt2.76 | 8xt2.77 | 8xt2.79 | 8xt2.80