SMTL ID : 3cx5.1

Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-1-mer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 14 residues within 4Å: Chain O: Y.137, D.139, E.140, P.141, L.147, G.150, S.151, N.152, Y.153, A.165, R.166 Chain W: K.16, L.20, Q.21 6 PLIP interactions: 4 interactions with chain O, 2 interactions with chain W Hydrogen bonds: O:G.150, O:G.150, O:N.152, O:Y.153, O:Y.153, O:R.166, W:K.16, W:K.16 Water bridges: O:Q.109, O:R.166

2 x 6PH: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate(Non-covalent)

6PH.2: 12 residues within 4Å: Chain A: S.424, M.429 Chain C: S.34, V.41, I.226, F.227, L.230, V.233 Chain E: V.30, M.33, S.37 Ligands: UMQ.3 12 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: C:V.41, C:I.226, C:F.227, C:L.230, C:V.233 Water bridges: C:H.222, C:S.223, D:K.230, D:K.230 Salt bridges: C:H.222, D:K.230 Hydrogen bonds: A:S.424 6PH.14: 16 residues within 4Å: Chain L: S.424, M.429 Chain N: S.34, L.38, I.226, F.227, D.229, L.230, V.233, F.234, M.237 Chain P: V.30, S.37 Ligands: CN5.9, UMQ.15, 7PH.23 15 PLIP interactions: 1 interactions with chain S, 10 interactions with chain N, 3 interactions with chain O, 1 interactions with chain L Water bridges: S:Y.31, N:H.222, N:S.223, O:K.230, O:K.230 Hydrophobic interactions: N:L.38, N:I.226, N:F.227, N:D.229, N:V.233, N:V.233, N:F.234 Salt bridges: N:H.222, O:K.230 Hydrogen bonds: L:S.424

2 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.3: 18 residues within 4Å: Chain A: W.401, D.402, S.427, M.428, M.429, R.430 Chain E: Y.27, V.30, G.34, S.38, A.41 Chain I: N.13, A.14, V.15, F.16, V.17, I.20 Ligands: 6PH.2 15 PLIP interactions: 5 interactions with chain A, 6 interactions with chain I, 4 interactions with chain E Hydrogen bonds: A:S.427, A:M.428, A:R.430, A:R.430, I:N.13, I:A.14, I:V.17, E:Y.27, E:Y.27, E:Y.27 Water bridges: A:D.402, I:V.15 Hydrophobic interactions: I:V.17, I:I.20, E:A.41 UMQ.15: 18 residues within 4Å: Chain L: W.401, D.402, S.427, M.428, M.429, R.430 Chain P: Y.27, V.30, S.37, S.38, A.41 Chain T: N.13, A.14, V.15, F.16, V.17, I.20 Ligands: 6PH.14 16 PLIP interactions: 2 interactions with chain S, 6 interactions with chain T, 4 interactions with chain L, 4 interactions with chain P Water bridges: S:Y.31, S:Y.31, T:V.15 Hydrophobic interactions: T:V.17, T:I.20, P:A.41 Hydrogen bonds: T:N.13, T:A.14, T:V.17, L:S.427, L:M.428, L:R.430, L:R.430, P:Y.27, P:Y.27, P:Y.27

7 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)(Covalent)

HEM.4: 23 residues within 4Å: Chain C: L.40, Q.43, I.44, G.47, I.48, M.50, A.51, V.65, R.79, H.82, A.83, A.86, F.89, T.127, A.128, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, Y.274 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:L.40, C:Q.43, C:A.51, C:V.65, C:A.83, C:A.86, C:F.89, C:T.127, C:Y.184 Salt bridges: C:R.79, C:R.79 pi-Stacking: C:H.82, C:H.183, C:H.183 Metal complexes: C:H.82, C:H.183 HEM.5: 23 residues within 4Å: Chain C: W.30, G.33, S.34, L.36, G.37, F.89, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, F.121, V.194, H.197, L.198, L.201, S.206, S.207 25 PLIP interactions: 25 interactions with chain C, Hydrophobic interactions: C:L.36, C:L.36, C:F.89, C:L.113, C:W.114, C:W.114, C:V.118, C:I.120, C:F.121, C:V.194, C:V.194, C:L.198, C:L.201 Hydrogen bonds: C:W.30, C:G.33, C:S.105, C:S.207 Water bridges: C:M.32, C:S.34 Salt bridges: C:H.96, C:K.99, C:K.99, C:R.110 Metal complexes: C:H.96, C:H.197 HEM.10: 20 residues within 4Å: Chain D: V.39, C.40, C.43, H.44, N.108, P.113, P.114, I.119, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167, L.168, L.194 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:P.113, D:P.114, D:I.119, D:I.130, D:L.133, D:L.134, D:L.134, D:I.162, D:A.163, D:M.164, D:V.167, D:L.168, D:L.194 Hydrogen bonds: D:Y.129, D:Y.129, D:A.163 Water bridges: D:R.123 Salt bridges: D:R.123 pi-Stacking: D:H.44 pi-Cation interactions: D:H.44 Metal complexes: D:H.44 HEM.16: 25 residues within 4Å: Chain N: L.40, Q.43, I.44, G.47, I.48, M.50, A.51, Y.54, V.65, R.79, H.82, A.83, A.86, F.89, T.127, A.128, G.131, Y.132, V.135, F.180, H.183, Y.184, P.187, I.190, Y.274 22 PLIP interactions: 22 interactions with chain N, Hydrophobic interactions: N:L.40, N:Q.43, N:I.44, N:I.48, N:A.51, N:Y.54, N:V.65, N:A.83, N:A.86, N:F.89, N:T.127, N:Y.184, N:Y.184, N:P.187, N:I.190 Water bridges: N:R.79 Salt bridges: N:R.79, N:R.79 pi-Stacking: N:H.82, N:H.183 Metal complexes: N:H.82, N:H.183 HEM.17: 22 residues within 4Å: Chain N: W.30, G.33, L.36, G.37, F.89, M.93, H.96, M.97, K.99, S.105, L.113, W.114, G.117, V.118, I.120, F.121, V.194, H.197, L.198, L.201, S.206, S.207 23 PLIP interactions: 23 interactions with chain N, Hydrophobic interactions: N:L.36, N:L.36, N:F.89, N:L.113, N:W.114, N:W.114, N:I.120, N:F.121, N:L.198, N:L.201 Hydrogen bonds: N:W.30, N:G.33, N:S.105, N:S.207 Water bridges: N:M.32, N:M.32, N:S.34 Salt bridges: N:H.96, N:K.99, N:K.99, N:R.110 Metal complexes: N:H.96, N:H.197 HEM.22: 20 residues within 4Å: Chain O: V.39, C.40, C.43, H.44, N.108, P.113, P.114, I.119, R.123, Y.129, I.130, L.133, L.134, F.157, I.162, A.163, M.164, V.167, L.168, L.194 20 PLIP interactions: 20 interactions with chain O, Hydrophobic interactions: O:P.113, O:I.119, O:I.130, O:L.133, O:L.134, O:L.134, O:I.162, O:A.163, O:M.164, O:V.167, O:L.168, O:L.194 Hydrogen bonds: O:Y.129, O:A.163 Water bridges: O:R.123 Salt bridges: O:R.123 pi-Stacking: O:H.44, O:H.44 pi-Cation interactions: O:H.44 Metal complexes: O:H.44 HEM.25: 27 residues within 4Å: Chain W: R.18, C.19, Q.21, C.22, H.23, V.33, G.34, P.35, L.37, I.40, S.45, G.46, Y.51, Y.53, T.54, N.57, W.64, M.69, Y.72, L.73, T.83, K.84, M.85, A.86, F.87, L.99, L.103 25 PLIP interactions: 25 interactions with chain W, Hydrophobic interactions: W:Q.21, W:V.33, W:P.35, W:L.37, W:L.37, W:I.40, W:Y.51, W:L.73, W:K.84, W:F.87, W:L.99, W:L.103 Hydrogen bonds: W:G.46, W:Y.53, W:T.54, W:N.57, W:T.83, W:K.84 Water bridges: W:R.43, W:R.43, W:Q.47 Salt bridges: W:K.84 pi-Stacking: W:H.23, W:Y.72 Metal complexes: W:H.23

2 x SMA: STIGMATELLIN A(Non-covalent)

SMA.6: 21 residues within 4Å: Chain C: I.122, I.125, F.129, L.130, M.139, G.143, V.146, I.147, F.151, F.179, I.269, P.271, E.272, L.275, F.278, Y.279, M.295, F.296, I.299 Chain P: C.150, H.151 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.125, C:F.129, C:F.129, C:L.130, C:I.147, C:F.151, C:F.179, C:F.278 Hydrogen bonds: C:E.272 Water bridges: C:E.272 SMA.18: 22 residues within 4Å: Chain E: C.150, H.151 Chain N: I.122, I.125, F.129, L.130, M.139, G.143, V.146, I.147, F.151, F.179, L.182, I.269, P.271, E.272, L.275, F.278, Y.279, M.295, F.296, I.299 9 PLIP interactions: 9 interactions with chain N Hydrophobic interactions: N:F.129, N:F.129, N:L.130, N:V.146, N:F.151, N:F.179, N:L.182, N:F.278 Hydrogen bonds: N:E.272

2 x 8PE: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate(Non-covalent)

8PE.7: 21 residues within 4Å: Chain C: W.29, M.91, F.94, M.95, A.98, K.99, Y.102, Y.103, F.278, L.302, T.317, F.326, F.327, F.329, V.330, F.331, F.333, Y.359 Chain G: E.81 Chain H: R.50, Q.54 15 PLIP interactions: 1 interactions with chain G, 11 interactions with chain C, 3 interactions with chain H Hydrogen bonds: G:E.81, C:Y.102, C:T.317, H:Q.54 Hydrophobic interactions: C:W.29, C:F.278, C:L.302, C:F.326, C:F.329, C:V.330, C:F.331, C:F.333 Water bridges: C:T.317, H:R.50 Salt bridges: H:R.50 8PE.19: 17 residues within 4Å: Chain N: W.29, F.94, M.95, A.98, Y.102, Y.103, F.121, F.278, L.302, T.317, F.326, F.327, V.330, F.331, F.333, Y.359 Chain R: E.81 17 PLIP interactions: 13 interactions with chain N, 2 interactions with chain R, 2 interactions with chain S Hydrophobic interactions: N:W.29, N:F.94, N:F.121, N:F.278, N:L.302, N:F.326, N:V.330, N:F.331, N:F.333, N:F.333, N:F.333 Hydrogen bonds: N:Y.103, N:T.317 Water bridges: R:E.81, R:E.81, S:Q.54, S:Q.54

2 x 9PE: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate(Non-covalent)

9PE.8: 12 residues within 4Å: Chain C: F.3, N.7, Y.9, L.10, V.13, I.195 Chain N: T.112, N.115, I.195, M.196, M.199 Ligands: CN5.9 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain N Hydrophobic interactions: C:L.10, C:V.13, C:I.195 Hydrogen bonds: C:N.7, N:N.115 Water bridges: C:V.8 9PE.20: 9 residues within 4Å: Chain C: P.109, T.112, N.115, A.192, M.196, M.199 Chain N: F.3, N.7, Y.9 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain N Hydrophobic interactions: C:A.192, N:Y.9 Hydrogen bonds: C:T.112, C:N.115, N:N.7 Water bridges: C:H.204, N:V.8

1 x CN5: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate(Non-covalent)

CN5.9: 13 residues within 4Å: Chain C: L.12, Y.16, M.199, H.202 Chain N: L.12, Y.16, I.17, I.195, M.199, H.202, D.229 Ligands: 9PE.8, 6PH.14 7 PLIP interactions: 4 interactions with chain N, 3 interactions with chain C Hydrophobic interactions: N:Y.16, N:Y.16, N:I.17 Hydrogen bonds: N:H.202, C:Y.16, C:Y.16 Salt bridges: C:H.202

2 x 7PH: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(Non-covalent)

7PH.11: 13 residues within 4Å: Chain C: I.42, M.237, F.245 Chain D: L.208, K.211, T.212, I.215, L.216 Chain E: G.40, A.41, S.43, T.44, T.47 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:T.44, D:L.216 Hydrogen bonds: E:S.43, D:T.212 Salt bridges: D:K.211 7PH.23: 13 residues within 4Å: Chain N: L.81, M.237, F.245 Chain O: L.208, K.211, T.212, I.215, L.216 Chain P: G.40, S.43, T.44, T.47 Ligands: 6PH.14 5 PLIP interactions: 2 interactions with chain N, 1 interactions with chain P, 2 interactions with chain O Hydrophobic interactions: N:L.81, N:M.237, O:L.216 Hydrogen bonds: P:S.43 Salt bridges: O:K.211

2 x CN3: (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate(Non-covalent)

CN3.12: 16 residues within 4Å: Chain C: N.27, Y.28, W.29, F.88, M.95, V.231, T.232, L.235, F.236, I.239 Chain D: Y.220, I.224, K.227, K.228 Chain G: H.84 Chain H: R.50 18 PLIP interactions: 8 interactions with chain D, 1 interactions with chain G, 8 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: D:I.224, C:Y.28, C:F.88, C:F.88, C:T.232, C:L.235, C:F.236, C:I.239 Hydrogen bonds: D:Y.220, C:Y.28 Water bridges: D:K.227, D:K.227 Salt bridges: D:K.227, D:K.228, D:K.228, D:K.235, G:H.84, H:R.50 CN3.21: 15 residues within 4Å: Chain N: N.27, Y.28, W.29, M.32, L.35, M.95, V.231, L.235, F.236 Chain O: Y.220, I.224, K.227, K.228 Chain R: H.84 Chain S: R.50 15 PLIP interactions: 7 interactions with chain O, 2 interactions with chain S, 5 interactions with chain N, 1 interactions with chain R Water bridges: O:K.227, O:K.227, O:K.235 Salt bridges: O:K.227, O:K.228, O:K.228, O:K.235, S:R.50, R:H.84 Hydrogen bonds: S:R.50, N:Y.28, N:Y.28 Hydrophobic interactions: N:L.35, N:L.235, N:F.236

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

FES.13: 10 residues within 4Å: Chain E: C.129, H.131, L.132, G.133, C.134, C.148, C.150, H.151, G.152, S.153 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.129, E:H.131, E:C.148, E:H.151 FES.24: 10 residues within 4Å: Chain P: C.129, H.131, L.132, G.133, C.134, C.148, C.150, H.151, G.152, S.153 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.129, P:H.131, P:C.148, P:H.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Solmaz, S.R. et al., Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer. J.Biol.Chem. (2008)

Release Date

2008-05-13

Peptides

Cytochrome b-c1 complex subunit 1, mitochondrial: AL
Cytochrome b-c1 complex subunit 2, mitochondrial: BM
CYTOCHROME B: CN
Cytochrome c1, heme protein, mitochondrial: DO
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EP
Cytochrome b-c1 complex subunit 6: FQ
Cytochrome b-c1 complex subunit 7: GR
Cytochrome b-c1 complex subunit 8: HS
Cytochrome b-c1 complex subunit 9: IT
HEAVY CHAIN (VH) OF FV-FRAGMENT: JU
LIGHT CHAIN (VL) OF FV-FRAGMENT: KV
Cytochrome c iso-1: W

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
L

B
B

M
M

C
C

N
N

D
D

O
O

E
E

P
P

F
F

Q
Q

G
G

R
R

H
H

S
S

I
I

T
T

J
J

U
U

K
K

V
V

W
W

Membrane

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

Cytochrome b-c1 complex subunit 1, mitochondrial

Cytochrome b-c1 complex subunit 2, mitochondrial

CYTOCHROME B

Cytochrome c1, heme protein, mitochondrial

Cytochrome b-c1 complex subunit Rieske, mitochondrial

Cytochrome b-c1 complex subunit 6

Cytochrome b-c1 complex subunit 7

Cytochrome b-c1 complex subunit 8

Cytochrome b-c1 complex subunit 9

HEAVY CHAIN (VH) OF FV-FRAGMENT

LIGHT CHAIN (VL) OF FV-FRAGMENT

Cytochrome c iso-1

Related Entries With Identical Sequence