SMTL ID : 4wz7.1

Crystal structure of mitochondrial NADH:ubiquinone oxidoreductase from Yarrowia lipolytica.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

hetero-oligomer

Ligands

6 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: unknown subunits(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 2 residues within 4Å: Chain 3: X.5 Chain W: X.29 No protein-ligand interaction detected (PLIP) UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.2: 6 residues within 4Å: Chain P: X.55, X.56, X.57 Chain V: X.59, X.63, X.66 No protein-ligand interaction detected (PLIP) UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.3: 4 residues within 4Å: Chain D: X.14 Chain h: X.62, X.63 Chain i: X.27 No protein-ligand interaction detected (PLIP) UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.4: 1 residues within 4Å: Chain K: Y.127 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Y.127 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.5: 1 residues within 4Å: Chain s: X.3 No protein-ligand interaction detected (PLIP) UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.6: 2 residues within 4Å: Chain u: X.18 Chain v: X.19 No protein-ligand interaction detected (PLIP)

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.7: 7 residues within 4Å: Chain G: X.32, X.33, C.34, X.35, C.45, X.46, C.59 3 PLIP interactions: 3 interactions with chain G, Metal complexes: G:C.34, G:C.45, G:C.59 FES.11: 9 residues within 4Å: Chain L: C.65, T.67, P.69, C.70, C.104, X.105, G.106, A.107, C.108 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.65, L:C.70, L:C.104, L:C.108

6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.8: 8 residues within 4Å: Chain G: A.91, C.92, C.95, A.96, C.101, X.190, G.191 Chain I: I.360 3 PLIP interactions: 3 interactions with chain G, Metal complexes: G:C.92, G:C.95, G:C.101 SF4.9: 7 residues within 4Å: Chain G: C.138, I.139, C.141, T.142, R.143, C.144, C.188 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.138, G:C.141, G:C.144, G:C.188 SF4.10: 7 residues within 4Å: Chain H: X.289, C.290, G.291, C.293, C.296, C.336, L.338 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.290, H:C.293, H:C.296, H:C.336 SF4.12: 11 residues within 4Å: Chain M: C.52, L.55, A.56, C.78, I.79, Y.80, C.81, G.82, Y.83, C.84, E.95 5 PLIP interactions: 5 interactions with chain M, Salt bridges: M:E.95 Metal complexes: M:C.52, M:C.78, M:C.81, M:C.84 SF4.13: 12 residues within 4Å: Chain M: X.41, C.42, I.43, A.44, C.45, L.47, C.48, Y.71, C.88, V.90, A.92, I.93 4 PLIP interactions: 4 interactions with chain M, Metal complexes: M:C.42, M:C.45, M:C.48, M:C.88 SF4.14: 10 residues within 4Å: Chain N: A.57, C.58, C.59, G.94, T.95, G.121, S.122, C.123, C.153, P.154 4 PLIP interactions: 4 interactions with chain N, Metal complexes: N:C.58, N:C.59, N:C.123, N:C.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zickermann, V. et al., Structural biology. Mechanistic insight from the crystal structure of mitochondrial complex I. Science (2015)

Release Date

2015-03-25

Peptides

NADH-ubiquinone oxidoreductase chain 1: A
NADH dehydrogenase subunit 2: B
NADH-ubiquinone oxidoreductase chain 3: C
NADH-ubiquinone oxidoreductase chain 4: D
NADH-ubiquinone oxidoreductase chain 5: E
NADH-ubiquinone oxidoreductase chain 6: F
NUAM protein: G
NUBM protein: H
NUCM protein: I
39-kDa subunit: J
NUGM protein: K
Subunit NUHM of protein NADH:Ubiquinone Oxidoreductase (Complex I): L
Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I): M
Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I): N
NADH-ubiquinone oxidoreductase chain 4L: O
unknown subunits 1: PQ
unknown subunits 2: R
unknown subunits: S
unknown subunits: T
unknown subunits: U
unknown subunits: V
unknown subunits: W
unknown subunits: X
unknown subunits: Y
unknown subunits: Z
unknown subunits: 0b
unknown subunits: 1
unknown subunits: 2
unknown subunits: 3dox
unknown subunits: 4km
unknown subunits: 5psw
unknown subunits: 67
unknown subunits: 8
unknown subunits: 9
unknown subunits: a
unknown subunits: cf
unknown subunits: eh
unknown subunits: g
unknown subunits: i
unknown subunits: jl
unknown subunits: n
unknown subunits: q
unknown subunits: r
unknown subunits: t
unknown subunits: uv
unknown subunits: y

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
A

H
B

I
C

J
E

K
G

L
H

M
I

N
K

O
L

P
Z

Q
D

R
F

S
J

T
M

U
N

V
O

W
P

X
Q

Y
R

Z
S

0
T

b
AH

1
U

2
V

3
X

d
AJ

o
AV

x
BH

4
Y

k
AR

m
AT

5
AA

p
AW

s
BB

w
BG

6
AC

7
AD

8
AE

9
AF

a
AG

c
AI

f
AL

e
AK

h
AN

g
AM

i
AO

j
AP

l
AS

n
AU

q
AX

r
AZ

t
BC

u
BD

v
BF

y
BI

Membrane

We predict this structure to be a membrane protein.
Show / Hide

NADH-ubiquinone oxidoreductase chain 1

NADH dehydrogenase subunit 2

NADH-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 6

NUAM protein

NUBM protein

NUCM protein

39-kDa subunit

NUGM protein

Subunit NUHM of protein NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I)

Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I)

NADH-ubiquinone oxidoreductase chain 4L

unknown subunits 1

unknown subunits 2

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

unknown subunits

Related Entries With Identical Sequence