SMTL ID : 3cwb.1

Chicken Cytochrome BC1 Complex inhibited by an iodinated analogue of the polyketide Crocacin-D

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

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

Ligands

6 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.1: 3 residues within 4Å: Chain A: Y.442 Chain C: H.222 Ligands: PEE.8 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.222, C:H.222 PEE.8: 14 residues within 4Å: Chain A: Y.442 Chain C: F.227, I.230 Chain D: M.222, K.226 Chain E: Y.37, T.40, C.44, T.47, K.52 Chain J: F.11, F.17, E.29 Ligands: PEE.1 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: J:F.17 Hydrogen bonds: E:Y.37 Salt bridges: D:K.226 PEE.9: 17 residues within 4Å: Chain C: W.31, F.96, L.97, Y.104, Y.105, F.277, T.317, F.326, W.327, V.330, L.333, L.334, T.337 Chain F: Y.29 Chain G: Q.44, V.48 Ligands: CDL.16 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.31, C:W.31, C:F.96, C:Y.104, C:Y.105, C:F.277, C:F.326, C:W.327, C:V.330, C:L.334 Hydrogen bonds: C:Y.104, C:Y.104, C:Y.105 PEE.25: 19 residues within 4Å: Chain M: W.31, F.96, L.97, G.100, Y.104, Y.105, F.277, T.317, F.326, W.327, V.330, L.333, L.334, T.337, Y.359 Chain P: Y.29 Chain Q: Q.44, V.48 Ligands: CDL.24 14 PLIP interactions: 13 interactions with chain M, 1 interactions with chain P Hydrophobic interactions: M:W.31, M:W.31, M:F.96, M:Y.104, M:Y.104, M:Y.105, M:F.277, M:F.326, M:W.327, M:V.330, M:L.333, M:L.334 Hydrogen bonds: M:Y.104, P:Y.29 PEE.26: 3 residues within 4Å: Chain K: Y.442 Chain M: H.222 Ligands: PEE.34 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain K Salt bridges: M:H.222 Hydrogen bonds: K:Y.442 PEE.34: 14 residues within 4Å: Chain K: Y.442 Chain M: F.227, I.230 Chain O: T.40, C.44, T.47, A.51, K.52 Chain T: F.11, R.12, T.14, A.18, E.29 Ligands: PEE.26 5 PLIP interactions: 3 interactions with chain O, 1 interactions with chain T, 1 interactions with chain K Hydrophobic interactions: O:T.47, O:A.51 Hydrogen bonds: O:T.40, T:R.12, K:Y.442

6 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.2: 6 residues within 4Å: Chain C: M.14, S.18, L.198, T.199, H.202 Ligands: UQ.7 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.198 Hydrogen bonds: C:S.18, C:T.199, C:T.199 Salt bridges: C:H.202 BOG.10: 8 residues within 4Å: Chain C: Y.76 Chain D: H.23, V.54, P.196, D.199, Q.200, R.203 Ligands: BOG.13 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.54, D:D.199 Hydrogen bonds: D:Q.200, D:R.203, C:Y.76 Salt bridges: D:R.203 BOG.13: 10 residues within 4Å: Chain C: Y.76 Chain D: Q.200, R.203, M.204, K.207 Chain E: A.50, N.53, Q.57 Chain J: D.37 Ligands: BOG.10 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E, 1 interactions with chain J, 1 interactions with chain C Hydrogen bonds: D:Q.200, E:N.53, J:D.37, C:Y.76 Salt bridges: D:K.207 Hydrophobic interactions: E:A.50 BOG.17: 8 residues within 4Å: Chain M: M.14, I.15, N.17, S.18, L.19, L.198, T.199, H.202 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:I.15, M:L.19, M:L.198 Hydrogen bonds: M:N.17, M:S.18 BOG.29: 11 residues within 4Å: Chain M: Y.76, L.241 Chain N: Q.200, R.203, M.204, K.207, I.211 Chain O: A.50, N.53, Q.57 Ligands: BOG.30 6 PLIP interactions: 3 interactions with chain N, 1 interactions with chain M, 2 interactions with chain O Hydrophobic interactions: N:I.211, M:L.241, O:A.50 Hydrogen bonds: N:Q.200, O:N.53 Salt bridges: N:K.207 BOG.30: 2 residues within 4Å: Chain N: Q.200 Ligands: BOG.29 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:Q.200, N:Q.200

2 x AZI: AZIDE ION(Non-covalent)

AZI.3: 3 residues within 4Å: Chain C: F.64, R.81, N.256 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.81, C:R.81, C:N.256 AZI.18: 3 residues within 4Å: Chain M: F.64, R.81, N.256 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:R.81, M:R.81

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

HEM.4: 21 residues within 4Å: Chain C: Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, R.81, H.84, A.85, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, Y.274 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:Q.45, C:I.46, C:L.52, C:L.52, C:A.53, C:Y.56, C:L.124, C:T.127, C:L.134, C:F.184, C:P.187 Salt bridges: C:R.81, C:R.81 Metal complexes: C:H.84, C:H.183 HEM.5: 24 residues within 4Å: Chain C: W.32, G.35, S.36, L.38, A.39, I.95, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, L.121, I.190, T.194, H.197, L.198, L.201, S.206, N.207 Ligands: UQ.7 23 PLIP interactions: 23 interactions with chain C, Hydrophobic interactions: C:L.38, C:I.95, C:I.99, C:T.113, C:W.114, C:W.114, C:V.118, C:L.120, C:L.121, C:I.190, C:L.198, C:L.201, C:L.201 Hydrogen bonds: C:G.35, C:N.207 Water bridges: C:W.32, C:R.101, C:S.206 Salt bridges: C:H.98, C:R.101, C:R.101 Metal complexes: C:H.98, C:H.197 HEM.19: 21 residues within 4Å: Chain M: Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, R.81, H.84, A.85, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, Y.274 15 PLIP interactions: 15 interactions with chain M, Hydrophobic interactions: M:Q.45, M:I.46, M:L.52, M:L.52, M:A.53, M:Y.56, M:L.124, M:T.127, M:L.134, M:F.184, M:P.187 Salt bridges: M:R.81, M:R.81 Metal complexes: M:H.84, M:H.183 HEM.20: 24 residues within 4Å: Chain M: W.32, G.35, S.36, L.38, A.39, I.95, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, L.121, I.190, T.194, H.197, L.198, L.201, S.206, N.207 Ligands: UQ.22 26 PLIP interactions: 26 interactions with chain M, Hydrophobic interactions: M:L.38, M:I.95, M:I.99, M:T.113, M:W.114, M:W.114, M:V.118, M:L.120, M:L.121, M:I.190, M:L.198, M:L.201, M:L.201 Hydrogen bonds: M:G.35, M:N.207 Water bridges: M:W.32, M:S.36, M:R.101, M:S.206 Salt bridges: M:H.98, M:R.101, M:R.101 pi-Stacking: M:H.98, M:H.98 Metal complexes: M:H.98, M:H.197

2 x ICX: methyl N-[(5Z)-6-({[4-(4-iodobenzyl)phenyl]carbonyl}amino)hex-5-enoyl]glycinate(Non-covalent)

ICX.6: 15 residues within 4Å: Chain C: A.126, Y.132, W.142, G.143, V.146, I.147, I.269, P.271, E.272, Y.274, F.275, A.278, Y.279, L.282 Chain O: H.161 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:V.146, C:I.147, C:I.147, C:I.269, C:I.269, C:F.275, C:F.275, C:A.278, C:L.282 Hydrogen bonds: C:E.272 pi-Stacking: C:F.275 ICX.21: 18 residues within 4Å: Chain E: H.161 Chain M: A.128, F.129, Y.132, W.142, G.143, V.146, I.147, I.269, K.270, P.271, E.272, Y.274, F.275, A.278, Y.279, L.282, L.295 11 PLIP interactions: 11 interactions with chain M Hydrophobic interactions: M:V.146, M:I.147, M:I.147, M:I.269, M:I.269, M:F.275, M:A.278, M:L.282, M:L.295 Hydrogen bonds: M:E.272 pi-Stacking: M:F.275

2 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)

UQ.7: 13 residues within 4Å: Chain C: S.18, L.22, P.23, I.28, S.36, A.39, L.198, H.202, S.206, F.221, D.229 Ligands: BOG.2, HEM.5 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.39, C:L.198, C:F.221 Hydrogen bonds: C:S.206 UQ.22: 11 residues within 4Å: Chain M: S.18, L.19, L.22, I.28, L.198, H.202, S.206, F.221, Y.225, D.229 Ligands: HEM.20 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:L.19, M:L.198, M:F.221 Hydrogen bonds: M:S.206 Water bridges: M:S.36

2 x HEC: HEME C(Covalent)

HEC.11: 21 residues within 4Å: Chain D: V.32, V.36, C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, I.116, R.120, Y.126, L.130, L.131, F.153, I.158, G.159, M.160, P.163, V.186 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:V.32, D:A.108, D:P.110, D:I.116, D:L.130, D:L.131, D:I.158, D:M.160, D:P.163, D:V.186 Hydrogen bonds: D:G.159 Salt bridges: D:R.120 pi-Stacking: D:H.41, D:H.41 Metal complexes: D:H.41 HEC.31: 21 residues within 4Å: Chain N: V.32, V.36, C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, L.113, R.120, Y.126, L.130, L.131, F.153, I.158, G.159, M.160, P.163, V.186 14 PLIP interactions: 14 interactions with chain N, Hydrophobic interactions: N:V.32, N:A.108, N:L.113, N:L.130, N:L.131, N:I.158, N:M.160, N:P.163, N:V.186 Hydrogen bonds: N:G.159 Salt bridges: N:R.120 pi-Stacking: N:H.41 pi-Cation interactions: N:H.41 Metal complexes: N:H.41

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.12: 15 residues within 4Å: Chain C: A.30, N.33, K.228, L.231, G.232, L.235 Chain D: Y.220, K.223, R.224 Chain F: H.72, R.73 Chain G: A.33, V.37, R.40 Ligands: CDL.16 8 PLIP interactions: 1 interactions with chain G, 3 interactions with chain C, 3 interactions with chain D, 1 interactions with chain F Hydrogen bonds: G:R.40, C:N.33 Hydrophobic interactions: C:A.30 Salt bridges: C:K.228, D:K.223, D:R.224, D:K.231, F:R.73 CDL.16: 10 residues within 4Å: Chain C: S.29, A.30, W.31, Y.105 Chain F: H.72 Chain G: R.40, F.41, Q.44 Ligands: PEE.9, CDL.12 7 PLIP interactions: 3 interactions with chain G, 3 interactions with chain C, 1 interactions with chain F Hydrogen bonds: G:R.40, C:A.30, C:Y.105 Salt bridges: G:R.40, G:R.40, F:H.72 Hydrophobic interactions: C:W.31 CDL.23: 15 residues within 4Å: Chain M: A.30, N.33, K.228, L.231, G.232, L.235 Chain N: Y.220, K.223, R.224, K.231 Chain P: H.72, R.73 Chain Q: L.34, R.40 Ligands: CDL.24 8 PLIP interactions: 3 interactions with chain N, 1 interactions with chain P, 2 interactions with chain M, 2 interactions with chain Q Salt bridges: N:K.223, N:R.224, N:K.231, P:R.73, M:K.228, Q:R.40 Hydrophobic interactions: M:A.30 Hydrogen bonds: Q:R.40 CDL.24: 11 residues within 4Å: Chain M: S.29, A.30, W.31, Y.105 Chain P: H.72 Chain Q: V.37, R.40, F.41, Q.44 Ligands: CDL.23, PEE.25 8 PLIP interactions: 3 interactions with chain M, 4 interactions with chain Q, 1 interactions with chain P Hydrophobic interactions: M:W.31, Q:V.37 Hydrogen bonds: M:A.30, M:Y.105, Q:R.40 Salt bridges: Q:R.40, Q:R.40, P:H.72

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

FES.14: 10 residues within 4Å: Chain E: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, G.162, S.163 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161 FES.33: 10 residues within 4Å: Chain O: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, G.162, S.163 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.139, O:H.141, O:C.158, O:H.161

4 x UNL: UNKNOWN LIGAND(Non-covalent)(Non-functional Binders)

UNL.15: 3 residues within 4Å: Chain D: M.204 Chain E: V.54, Q.57 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.57, E:Q.57 UNL.27: 4 residues within 4Å: Chain M: L.241 Chain O: V.54 Ligands: UNL.28, UNL.32 No protein-ligand interaction detected (PLIP) UNL.28: 1 residues within 4Å: Ligands: UNL.27 No protein-ligand interaction detected (PLIP) UNL.32: 3 residues within 4Å: Chain N: M.204 Chain O: Q.57 Ligands: UNL.27 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:Q.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crowley, P.J. et al., The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D. Bioorg.Med.Chem. (2008)

Release Date

2008-08-12

Peptides

MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I: AK
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2: BL
Cytochrome b: CM
MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN: DN
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN: EO
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN: FP
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C: GQ
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII: HR
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence: IS
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
N

B
B

L
O

C
C

M
P

D
D

N
Q

E
E

O
R

F
F

P
S

G
G

Q
T

H
H

R
U

I
I

S
V

J
J

T
W

Membrane

We predict this structure to be a membrane protein.
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MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I

MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2

Cytochrome b

MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN

MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN

MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN

MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C

MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII

MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence

MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN

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