SMTL ID : 8d4t.1

Mammalian CIV with GDN bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

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

Ligands

3 x CU: COPPER (II) ION(Non-covalent)

CU.1: 3 residues within 4Å: Chain A: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291 CU.7: 6 residues within 4Å: Chain B: H.161, C.196, C.200, H.204, M.207 Ligands: CU.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.200 CU.8: 7 residues within 4Å: Chain B: H.161, C.196, E.198, I.199, C.200, H.204 Ligands: CU.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.196, B:E.198, B:C.200, B:H.204

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.198, A:H.368, A:D.369

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 7 residues within 4Å: Chain A: E.40, L.41, Q.43, G.45, T.46, S.441, D.442 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.45

2 x HEA: HEME-A(Non-covalent)

HEA.4: 46 residues within 4Å: Chain A: L.20, G.23, A.24, G.27, M.28, T.31, S.34, I.37, R.38, L.41, Y.54, V.58, T.59, H.61, A.62, M.65, I.66, M.69, V.70, I.73, G.125, W.126, L.246, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, I.389, M.390, F.393, M.417, V.421, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, S.461, V.465, M.468 Ligands: HEA.5 35 PLIP interactions: 35 interactions with chain A, Hydrophobic interactions: A:A.24, A:I.37, A:R.38, A:A.62, A:M.65, A:I.66, A:V.70, A:I.73, A:V.374, A:F.377, A:L.381, A:L.381, A:V.386, A:V.386, A:F.393, A:F.393, A:T.424, A:V.465 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, A:S.382, A:Q.428, A:R.439, A:Y.440 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:H.61, A:F.377, A:H.378, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.5: 43 residues within 4Å: Chain A: W.126, T.127, W.236, H.240, V.243, Y.244, L.246, I.247, H.290, H.291, F.293, T.309, I.312, A.313, T.316, G.317, V.320, F.321, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, D.369, V.373, H.376, F.377, V.380, L.381, A.385, R.438 Chain B: I.34, V.38, P.69, I.72, L.73, I.76 Ligands: HEA.4 24 PLIP interactions: 19 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:A.313, A:F.348, A:F.377, A:F.377, A:V.380, A:L.381, B:I.34, B:I.34, B:I.72, B:L.73, B:L.73 Hydrogen bonds: A:W.126, A:Y.244, A:H.291 Salt bridges: A:H.368, A:R.438 pi-Cation interactions: A:H.240 Metal complexes: A:H.376

2 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.6: 38 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, L.104, H.151, L.152, V.155, I.158, L.159, I.162, P.200 Chain C: H.6, V.8, G.17, A.21, M.24, T.25, L.28, N.47, T.50, M.51, W.54, W.55, V.58, E.61, H.68, V.72, L.76, G.79, M.80, F.83, S.86, E.87, F.90 Ligands: PEK.9, PGV.10 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:A.21, C:T.25, C:W.54, C:W.54, C:F.83, C:F.83, C:F.90, A:L.152, A:V.155 Hydrogen bonds: C:H.6, C:W.54, C:W.55, C:E.61, C:H.68, A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.10: 28 residues within 4Å: Chain C: M.48, M.51, W.55, V.58, I.59, S.62, T.63, H.68, L.76, M.80, F.83, E.87, H.204, I.206, I.207, T.210, F.211, V.214, R.218, H.223, F.224, T.225, H.228, H.229, F.230, G.231 Chain F: Q.9 Ligands: PGV.6 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:W.55, C:W.55, C:W.55, C:W.55, C:W.55, C:W.55, C:W.55, C:W.55, C:I.59, C:I.207, C:I.207, C:I.207, C:F.211, C:F.211 Hydrogen bonds: C:T.63, C:R.218, C:F.230, C:G.231 Salt bridges: C:H.68, C:R.218, C:R.218, C:H.228

1 x PEK: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE(Non-covalent)

PEK.9: 36 residues within 4Å: Chain A: F.148, H.151, V.155, A.203, T.207, L.210, T.211, L.215 Chain C: L.28, W.31, F.32, F.90, T.171, Q.174, A.175, Y.178, Y.179, A.181, F.183, T.184, I.185, F.195, V.196, G.199, F.200, G.202, L.203, I.206 Chain G: W.51, T.57, F.58, F.59, H.60, N.61, N.65 Ligands: PGV.6 21 PLIP interactions: 7 interactions with chain G, 5 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: G:F.58, G:F.59, A:H.151, A:V.155, A:A.203, A:L.210, A:L.215, C:W.31, C:F.32, C:F.90, C:Q.174, C:I.185, C:F.200, C:F.200 Hydrogen bonds: G:T.57, G:F.58, G:F.59, G:F.59, G:N.65, C:A.181, C:I.185

1 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Covalent)

9Z9.11: 16 residues within 4Å: Chain A: I.169, N.170, Q.178, Y.179, W.186, M.189, I.190, V.193, L.194, L.197, M.278, G.281, F.282, F.285 Chain C: K.74, Y.78 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.178, A:W.186, A:I.190, A:V.193, A:V.193, A:L.194, A:F.285

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 6 residues within 4Å: Chain F: C.57, C.59, C.79, S.81, C.82, T.84 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.57, F:C.59, F:C.79, F:C.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Di Trani, J.M. et al., Structural basis of mammalian complex IV inhibition by steroids. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-07-06

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial: D
Cytochrome c oxidase subunit 5A, mitochondrial: E
Cytochrome c oxidase subunit 5B, mitochondrial: F
Cytochrome c oxidase subunit 6A2, mitochondrial: G
Cytochrome c oxidase subunit 6B1: H
Cytochrome c oxidase subunit 6C: I
Cytochrome c oxidase subunit 7A1, mitochondrial: J
Cytochrome c oxidase subunit 7B, mitochondrial: K
Cytochrome c oxidase subunit 7C, mitochondrial: L
Cytochrome c oxidase subunit 8A, mitochondrial: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
O

C
P

D
Q

E
R

F
S

G
T

H
U

I
V

J
W

K
X

L
Y

M
M

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 5B, mitochondrial

Cytochrome c oxidase subunit 6A2, mitochondrial

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7A1, mitochondrial

Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8A, mitochondrial

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