- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 3 x UNK- UNK- UNK- UNK- UNK: Unknown Protein(Non-covalent)
- 4 x ZN: ZINC ION(Non-covalent)
ZN.4: 4 residues within 4Å:- Chain A: C.291, C.294, C.304, H.323
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:C.291, A:C.294, A:C.304, A:H.323
ZN.5: 4 residues within 4Å:- Chain K: C.98, C.101, C.119, C.122
4 PLIP interactions:4 interactions with chain K- Metal complexes: K:C.98, K:C.101, K:C.119, K:C.122
ZN.6: 4 residues within 4Å:- Chain K: C.175, C.178, C.211, C.214
4 PLIP interactions:4 interactions with chain K- Metal complexes: K:C.175, K:C.178, K:C.211, K:C.214
ZN.12: 4 residues within 4Å:- Chain s: H.55, C.59, C.82, C.85
4 PLIP interactions:4 interactions with chain s- Metal complexes: s:H.55, s:C.59, s:C.82, s:C.85
- 1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)
UTP.7: 12 residues within 4Å:- Chain R: R.188
- Chain U: R.132, K.171, F.202, K.205, R.209, E.234, R.236, K.283, L.284, R.285
- Chain u: U.429
16 PLIP interactions:14 interactions with chain U, 2 interactions with chain R- Hydrogen bonds: U:K.205, U:E.234, U:R.236, U:R.285, R:R.188
- Salt bridges: U:R.132, U:R.132, U:K.171, U:K.205, U:K.205, U:K.205, U:R.209, U:R.236, U:R.285, R:R.188
- pi-Cation interactions: U:R.236
- 39 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.8: 4 residues within 4Å:- Chain 8: F.3
- Chain N: H.12
- Chain c: H.39, V.41
2 PLIP interactions:1 interactions with chain c, 1 interactions with chain N- Metal complexes: c:H.39, N:H.12
MG.9: 3 residues within 4Å:- Chain 4: M.67
- Chain B: G.766
- Chain h: R.363
No protein-ligand interaction detected (PLIP)MG.11: 3 residues within 4Å:- Ligands: GTP.10
- Chain k: S.156, T.358
4 PLIP interactions:1 interactions with chain k, 3 Ligand-Water interactions- Metal complexes: k:S.156, H2O.1, H2O.1, H2O.1
MG.13: 2 residues within 4Å:- Chain t: D.30
- Chain u: U.383
1 PLIP interactions:1 interactions with chain t- Metal complexes: t:D.30
MG.14: 1 residues within 4Å:- Chain u: A.27
No protein-ligand interaction detected (PLIP)MG.15: 2 residues within 4Å:- Chain u: U.65, A.131
No protein-ligand interaction detected (PLIP)MG.16: 3 residues within 4Å:- Chain u: U.65, U.66, A.133
No protein-ligand interaction detected (PLIP)MG.17: 3 residues within 4Å:- Chain u: A.60, A.61, A.155
No protein-ligand interaction detected (PLIP)MG.18: 3 residues within 4Å:- Chain u: A.68, A.93, U.94
No protein-ligand interaction detected (PLIP)MG.19: 2 residues within 4Å:- Chain u: U.69, A.91
No protein-ligand interaction detected (PLIP)MG.20: 3 residues within 4Å:- Chain a: D.405, N.429
- Chain u: A.91
No protein-ligand interaction detected (PLIP)MG.21: 4 residues within 4Å:- Chain u: G.141, U.142, U.143, G.147
No protein-ligand interaction detected (PLIP)MG.22: 3 residues within 4Å:- Chain u: U.231, G.232, U.246
No protein-ligand interaction detected (PLIP)MG.23: 2 residues within 4Å:- Chain u: C.237, U.251
No protein-ligand interaction detected (PLIP)MG.24: 3 residues within 4Å:- Chain u: U.338, U.339, A.355
No protein-ligand interaction detected (PLIP)MG.25: 2 residues within 4Å:- Chain u: A.571, A.572
No protein-ligand interaction detected (PLIP)MG.26: 2 residues within 4Å:- Chain u: U.563, U.564
No protein-ligand interaction detected (PLIP)MG.27: 1 residues within 4Å:- Chain u: A.603
No protein-ligand interaction detected (PLIP)MG.28: 1 residues within 4Å:- Chain u: U.606
No protein-ligand interaction detected (PLIP)MG.29: 2 residues within 4Å:- Chain u: U.592, A.593
No protein-ligand interaction detected (PLIP)MG.30: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.31: 3 residues within 4Å:- Chain u: A.280, U.281, A.367
No protein-ligand interaction detected (PLIP)MG.32: 3 residues within 4Å:- Ligands: MG.38
- Chain u: A.595, U.596
No protein-ligand interaction detected (PLIP)MG.33: 2 residues within 4Å:- Chain u: G.158, G.159
No protein-ligand interaction detected (PLIP)MG.34: 2 residues within 4Å:- Chain u: C.238, U.241
No protein-ligand interaction detected (PLIP)MG.35: 4 residues within 4Å:- Chain u: C.582, A.583, G.584, U.588
No protein-ligand interaction detected (PLIP)MG.36: 6 residues within 4Å:- Ligands: MG.37
- Chain u: G.584, A.587, U.588, A.590, A.591
No protein-ligand interaction detected (PLIP)MG.37: 5 residues within 4Å:- Ligands: MG.36
- Chain u: A.583, G.584, A.591, A.604
No protein-ligand interaction detected (PLIP)MG.38: 2 residues within 4Å:- Ligands: MG.32
- Chain p: Q.170
No protein-ligand interaction detected (PLIP)MG.39: 3 residues within 4Å:- Chain u: A.222, A.224, A.225
No protein-ligand interaction detected (PLIP)MG.40: 3 residues within 4Å:- Chain u: G.229, A.248, U.250
No protein-ligand interaction detected (PLIP)MG.41: 3 residues within 4Å:- Chain c: Q.15
- Chain q: Q.11
- Chain u: A.33
No protein-ligand interaction detected (PLIP)MG.42: 4 residues within 4Å:- Chain i: Y.9
- Chain u: G.542, A.586, U.613
No protein-ligand interaction detected (PLIP)MG.43: 2 residues within 4Å:- Chain u: A.386, U.387
No protein-ligand interaction detected (PLIP)MG.44: 2 residues within 4Å:- Chain u: A.385, U.544
No protein-ligand interaction detected (PLIP)MG.45: 3 residues within 4Å:- Chain i: K.13
- Chain o: D.68
- Chain u: A.541
No protein-ligand interaction detected (PLIP)MG.46: 5 residues within 4Å:- Chain m: R.10
- Chain u: A.75, A.76, A.77, G.78
No protein-ligand interaction detected (PLIP)MG.47: 2 residues within 4Å:- Chain 9: E.27
- Chain u: U.415
No protein-ligand interaction detected (PLIP)MG.48: 1 residues within 4Å:- Chain u: G.470
No protein-ligand interaction detected (PLIP)- 1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)
GTP.10: 23 residues within 4Å:- Ligands: MG.11
- Chain k: 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
22 PLIP interactions:22 interactions with chain k- Hydrogen bonds: k:R.96, k:V.97, k:Q.99, k:T.100, k:L.110, k:L.110, k:G.152, k:K.155, k:S.156, k:S.156, k:A.157, k:T.358, k:T.358, k:R.359
- Water bridges: k:G.95, k:S.156, k:S.156, k:S.156, k:D.286
- Salt bridges: k:K.155, k:K.155
- pi-Stacking: k:F.404
- 4 x SPD: SPERMIDINE(Non-covalent)
SPD.49: 10 residues within 4Å:- Chain 6: M.387
- Chain D: R.292
- Chain u: A.452, A.453, G.454, G.466, A.467, A.468, A.469, G.470
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain 6- Hydrogen bonds: D:R.292, 6:M.387
SPD.50: 5 residues within 4Å:- Chain 7: G.19
- Chain D: H.267
- Chain u: U.398, A.399, A.459
No protein-ligand interaction detected (PLIP)SPD.51: 10 residues within 4Å:- Chain h: R.572, D.578
- Chain q: Y.13, P.15
- Chain u: A.218, U.259, U.261, A.262, A.263, A.264
1 PLIP interactions:1 interactions with chain h- Hydrogen bonds: h:N.581
SPD.52: 12 residues within 4Å:- Chain 8: F.2, M.6, G.71, G.72
- Chain q: D.10, T.12
- Chain u: A.27, U.28, G.239, A.266, U.267, U.268
2 PLIP interactions:1 interactions with chain 8, 1 interactions with chain q- Hydrogen bonds: 8:F.2, q:T.12
- 1 x SPM: SPERMINE(Non-covalent)
- 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
mS51: B
mS56: C
mS59: D
mS60: E
mS61: F
mS62: G
mS63: H
mS64: I
mS65: J
mS66: K
mS68: L
mS73: M
mS74: N
mS49: O
mS50: P
mS52: Q
mS53: R
mS54: S
mS55: T
mS57: U
mS58: V
mS67: W
mS69: X
mS70: Y
mS71: Z
mS72: 0
uS3m: 1
uS5m: 2
bS6m: 3
uS8m: 4
uS9m: 5
uS10m: 6
uS11m: 7
uS12m: 8
uS14m: 9
uS15m: a
bS16m: b
uS17m: c
bS18m: d
uS19m: e
bS21m: f
mt-IF-3: g
mS22: h
mS23: i
mS26: j
mS29: k
mS33: l
mS34: m
mS35: n
mS37: o
mS38: p
mS41: q
mS42: r
mS43: s
mS47: t
Unknown Protein: v
Unknown Protein: w
Unknown Protein: x - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DAB
DDC
DID
DLE
DMF
DNG
DOH
DPI
DQJ
DRK
DSL
DUM
DZN
DaO
DBP
DCQ
DER
DFS
DGT
DHU
DJV
DKW
DTX
DVY
DWZ
DX0
DY1
CC2
CE3
CF4
CH5
CI6
CJ7
CK8
CL9
CNa
COb
CPc
CQd
CRe
CSf
CUg
CZh
Cai
Cbj
Cdk
Cgl
Cim
Cjn
Cko
Cmp
Cnq
Cpr
Cqs
Crt
Cvv
UQw
USx
UT
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 3 x UNK- UNK- UNK- UNK- UNK: Unknown Protein(Non-covalent)
- 4 x ZN: ZINC ION(Non-covalent)
- 1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)
- 39 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 4 x SPD: SPERMIDINE(Non-covalent)
- 1 x SPM: SPERMINE(Non-covalent)
- 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
mS51: B
mS56: C
mS59: D
mS60: E
mS61: F
mS62: G
mS63: H
mS64: I
mS65: J
mS66: K
mS68: L
mS73: M
mS74: N
mS49: O
mS50: P
mS52: Q
mS53: R
mS54: S
mS55: T
mS57: U
mS58: V
mS67: W
mS69: X
mS70: Y
mS71: Z
mS72: 0
uS3m: 1
uS5m: 2
bS6m: 3
uS8m: 4
uS9m: 5
uS10m: 6
uS11m: 7
uS12m: 8
uS14m: 9
uS15m: a
bS16m: b
uS17m: c
bS18m: d
uS19m: e
bS21m: f
mt-IF-3: g
mS22: h
mS23: i
mS26: j
mS29: k
mS33: l
mS34: m
mS35: n
mS37: o
mS38: p
mS41: q
mS42: r
mS43: s
mS47: t
Unknown Protein: v
Unknown Protein: w
Unknown Protein: x - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DAB
DDC
DID
DLE
DMF
DNG
DOH
DPI
DQJ
DRK
DSL
DUM
DZN
DaO
DBP
DCQ
DER
DFS
DGT
DHU
DJV
DKW
DTX
DVY
DWZ
DX0
DY1
CC2
CE3
CF4
CH5
CI6
CJ7
CK8
CL9
CNa
COb
CPc
CQd
CRe
CSf
CUg
CZh
Cai
Cbj
Cdk
Cgl
Cim
Cjn
Cko
Cmp
Cnq
Cpr
Cqs
Crt
Cvv
UQw
USx
UT