SMTL ID : 3j7y.1

Structure of the large ribosomal subunit from human mitochondria

Coordinates

PDB Format Compare

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-mer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-functional Binders)

AMP.1: 5 residues within 4Å: Chain A: U.1228, C.1229, G.1239, A.1240, A.1249 No protein-ligand interaction detected (PLIP)

66 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: U.1194, C.1195, A.1196, C.1197 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: U.178, U.350 Chain K: K.48, Q.58 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: A.87, U.88 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: A.52, A.53, C.55, C.56 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: G.106, U.108 Chain E: G.148 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain A: A.144, A.145, G.146 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: A.105, G.106, A.109 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: C.272, A.301 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain A: A.247, G.248 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: U.280, A.833, A.834 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: G.338, G.339, U.340, G.341 Chain g: K.112 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain A: C.322, A.323, A.324, A.1406 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain A: A.357, G.358 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain A: U.471, C.582, U.583 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain A: U.480, A.580 Chain P: R.65 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: A.290, A.291, A.760 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain A: U.752, C.753, A.754 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain A: G.822, C.824, A.836 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain A: G.647, A.780, A.781, A.782, G.783 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain A: A.837, C.838 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain A: G.783 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain A: C.987, U.988, U.990 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain A: A.643, A.998 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain A: G.1054, C.1318, G.1319 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain A: A.627, A.628, G.630 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain A: G.1264, C.1318, G.1319 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain A: U.350, A.627 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain A: C.51, C.56, G.1063 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Chain A: G.236 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain A: A.1256, A.1404, G.1405 No protein-ligand interaction detected (PLIP) MG.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain A: G.826, A.974 No protein-ligand interaction detected (PLIP) MG.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain A: U.932, C.933, A.934 No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain A: A.1002, G.1003, U.1004 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain A: A.798, A.799 Chain O: S.230 No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain A: A.777, G.778 Chain n: R.62 No protein-ligand interaction detected (PLIP) MG.39: 4 residues within 4Å: Chain A: G.1046, U.1392, G.1393, A.1394 No protein-ligand interaction detected (PLIP) MG.40: 5 residues within 4Å: Chain A: A.270, G.271, A.301, A.302, G.303 No protein-ligand interaction detected (PLIP) MG.41: 3 residues within 4Å: Chain A: A.324, G.332, G.1405 No protein-ligand interaction detected (PLIP) MG.42: 4 residues within 4Å: Chain A: A.803, C.804, U.805, U.1367 No protein-ligand interaction detected (PLIP) MG.43: 2 residues within 4Å: Chain A: A.839 Chain C: G.273 No protein-ligand interaction detected (PLIP) MG.44: 4 residues within 4Å: Chain A: A.1055, U.1260, A.1261 Chain E: K.131 No protein-ligand interaction detected (PLIP) MG.45: 6 residues within 4Å: Chain A: U.875, G.876, C.877, A.894, A.962, A.963 No protein-ligand interaction detected (PLIP) MG.46: 3 residues within 4Å: Chain A: A.798, A.799, G.985 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain A: G.1049, A.1050 No protein-ligand interaction detected (PLIP) MG.48: 3 residues within 4Å: Chain A: U.1059, U.1142, U.1143 No protein-ligand interaction detected (PLIP) MG.49: 3 residues within 4Å: Chain A: C.55, G.1062, G.1063 No protein-ligand interaction detected (PLIP) MG.50: 3 residues within 4Å: Chain A: G.1145, G.1146 Chain L: R.139 No protein-ligand interaction detected (PLIP) MG.51: 5 residues within 4Å: Chain A: G.181, A.1023, A.1265, C.1316, U.1317 No protein-ligand interaction detected (PLIP) MG.52: 1 residues within 4Å: Chain A: A.1288 No protein-ligand interaction detected (PLIP) MG.53: 4 residues within 4Å: Chain A: G.1264, A.1265, C.1315, C.1316 No protein-ligand interaction detected (PLIP) MG.54: 2 residues within 4Å: Chain A: A.1335, U.1336 No protein-ligand interaction detected (PLIP) MG.55: 3 residues within 4Å: Chain A: G.1393, C.1396, U.1428 No protein-ligand interaction detected (PLIP) MG.56: 3 residues within 4Å: Chain A: A.639, U.641, U.1432 No protein-ligand interaction detected (PLIP) MG.57: 1 residues within 4Å: Chain A: A.1205 No protein-ligand interaction detected (PLIP) MG.58: 1 residues within 4Å: Chain A: U.1368 No protein-ligand interaction detected (PLIP) MG.59: 2 residues within 4Å: Chain A: C.809, A.810 No protein-ligand interaction detected (PLIP) MG.60: 5 residues within 4Å: Chain A: U.280, C.281, A.834, G.1424, G.1425 No protein-ligand interaction detected (PLIP) MG.61: 1 residues within 4Å: Chain A: C.252 No protein-ligand interaction detected (PLIP) MG.62: 2 residues within 4Å: Chain A: G.370, A.427 No protein-ligand interaction detected (PLIP) MG.63: 4 residues within 4Å: Chain A: U.365, C.366, G.1247, A.1248 No protein-ligand interaction detected (PLIP) MG.64: 3 residues within 4Å: Chain A: A.237, A.342, U.343 No protein-ligand interaction detected (PLIP) MG.65: 3 residues within 4Å: Chain A: C.430, C.444, U.445 No protein-ligand interaction detected (PLIP) MG.66: 1 residues within 4Å: Chain A: U.445 No protein-ligand interaction detected (PLIP) MG.67: 6 residues within 4Å: Chain A: A.283, U.284, A.792, A.793 Chain D: T.234, H.237 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.68: 5 residues within 4Å: Chain Y: C.110, E.112, C.113, C.123, C.126 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.110, Y:C.113, Y:C.123, Y:C.126 ZN.69: 4 residues within 4Å: Chain 2: C.76, C.79, C.92, H.98 3 PLIP interactions: 3 interactions with chain 2 Metal complexes: 2:C.76, 2:C.79, 2:C.92 ZN.70: 4 residues within 4Å: Chain G: C.64 Chain m: C.70, C.73, C.108 2 PLIP interactions: 2 interactions with chain m Metal complexes: m:C.70, m:C.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brown, A. et al., Structure of the large ribosomal subunit from human mitochondria. Science (2014)

Release Date

2014-10-15

Peptides

uL2: C
uL3: D
uL4: E
bL9: F
uL10: G
uL11: H
uL13: I
uL14: J
uL15: K
uL16: L
bL17: M
uL18: N
bL19: O
bL20: P
bL21: Q
uL22: R
uL23: S
uL24: T
bL27: U
bL28: V
uL29: W
uL30: X
bL32: Y
bL33: Z
bL34: 0
bL35: 1
bL36: 2
mL37: 3
mL38: 4
mL39: 5
mL40: 6
mL41: 7
mL42: 8
mL43: 9
mL44: a
mL45: b
mL46: c
mL48: d
mL49: e
mL50: f
mL51: g
mL52: h
mL53: i
mL63: j
ICT1: k
CRIF1: l
bS18a: m
mS30: n
unknown protein: o

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
D

D
E

E
F

F
H

G
I

H
J

I
K

J
L

K
M

L
N

M
O

N
P

O
Q

P
R

Q
S

R
T

S
U

T
V

U
W

V
X

W
Y

X
Z

Y
0

Z
1

0
2

1
3

2
4

3
5

4
6

5
7

6
8

7
9

8
a

9
b

a
c

b
d

c
e

d
f

e
g

f
h

g
i

h
j

i
k

j
o

k
p

l
q

m
r

n
s

o
t

uL2

uL3

uL4

bL9

uL10

uL11

uL13

uL14

uL15

uL16

bL17

uL18

bL19

bL20

bL21

uL22

uL23

uL24

bL27

bL28

uL29

uL30

bL32

bL33

bL34

bL35

bL36

mL37

mL38

mL39

mL40

mL41

mL42

mL43

mL44

mL45

mL46

mL48

mL49

mL50

mL51

mL52

mL53

mL63

ICT1

CRIF1

bS18a

mS30

unknown protein

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