SMTL ID : 3ehb.1

A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

HEA.1: 35 residues within 4Å: Chain A: L.36, A.39, G.40, V.47, T.50, M.53, R.54, W.87, I.91, H.94, G.95, M.98, M.99, V.102, V.103, A.106, G.163, W.164, Y.406, F.412, H.413, M.416, S.417, V.421, F.425, M.452, I.459, F.460, Q.463, R.473, R.474, Y.475, S.496, F.500, F.503 35 PLIP interactions: 35 interactions with chain A, Hydrophobic interactions: A:T.50, A:I.91, A:M.98, A:V.102, A:V.103, A:A.106, A:F.412, A:V.421, A:V.421, A:F.425, A:I.459, A:F.460, A:F.460, A:F.500, A:F.500, A:F.500, A:F.503 Hydrogen bonds: A:R.54, A:W.87, A:W.164, A:Y.406, A:Q.463, A:R.474, A:Y.475 Water bridges: A:R.473, A:R.474 Salt bridges: A:R.473, A:R.474 pi-Stacking: A:H.94, A:H.94, A:H.413, A:H.413, A:F.460 Metal complexes: A:H.94, A:H.413 HEA.2: 30 residues within 4Å: Chain A: W.164, W.272, V.279, Y.280, H.325, H.326, T.344, A.348, T.351, G.352, V.355, F.356, F.383, G.387, V.388, G.390, V.391, L.393, S.394, D.399, H.403, V.408, H.411, F.412, V.415, M.416, R.473 Chain B: V.74, I.117 Ligands: PER.18 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:W.272, A:V.279, A:V.279, A:T.344, A:A.348, A:V.355, A:F.356, A:F.356, A:F.383, A:V.388, A:V.391, A:L.393, A:L.393, A:V.408, A:F.412, A:F.412, A:V.415, B:I.117 Hydrogen bonds: A:D.399 Water bridges: A:D.404, A:R.473, A:R.473 Salt bridges: A:H.403, A:R.473 pi-Cation interactions: A:H.276 Metal complexes: A:H.411

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

CU.3: 4 residues within 4Å: Chain A: H.276, H.325, H.326 Ligands: PER.18 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.276, A:H.325, A:H.326 CU.19: 5 residues within 4Å: Chain B: C.245, E.247, C.249, H.253 Ligands: CU.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.245, B:E.247, B:C.249, B:H.253 CU.20: 5 residues within 4Å: Chain B: H.210, C.245, C.249, M.256 Ligands: CU.19 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.210, B:C.245, B:C.249

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: H.403, D.404 Chain B: D.222, E.247 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.247, A:H.403, H2O.1, H2O.5, H2O.5

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: E.56, H.59, G.61, V.62, Q.63 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.56, A:E.56, A:H.59, A:G.61, H2O.4

9 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.6: 6 residues within 4Å: Chain A: L.458, Y.484, W.485, I.488 Ligands: LMT.14, LMT.27 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.458, A:W.485 LDA.7: 5 residues within 4Å: Chain A: C.48, V.51, M.55, L.72 Ligands: LMT.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.51, A:L.72 LDA.8: 2 residues within 4Å: Chain A: H.269, Q.336 No protein-ligand interaction detected (PLIP) LDA.9: 6 residues within 4Å: Chain A: W.22, L.34, F.37, L.511, F.512 Ligands: LMT.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.22, A:W.22, A:L.34, A:F.37, A:F.512 LDA.21: 5 residues within 4Å: Chain A: F.465, R.468 Chain B: N.48, L.68 Ligands: LDA.24 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.68, A:F.465 LDA.22: 7 residues within 4Å: Chain B: H.65, F.66, Y.69, I.70, L.116, I.117, A.120 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.66, B:F.66, B:Y.69, B:Y.69, B:I.70, B:L.116, B:I.117, B:A.120 LDA.23: 7 residues within 4Å: Chain A: F.356 Chain B: F.77, I.106, I.109, W.110, V.113 Ligands: LMT.28 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.77, B:F.77, B:V.113, A:F.356 LDA.24: 7 residues within 4Å: Chain B: H.65, L.68, Y.69, T.72, T.75 Ligands: LDA.21, LMT.27 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.68, B:Y.69 Water bridges: B:H.65 LDA.25: 3 residues within 4Å: Chain B: A.123 Ligands: LMT.26, LMT.29 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.124

12 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.10: 4 residues within 4Å: Chain A: W.443, L.447, F.502 Ligands: LMT.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.443, A:L.447, A:F.502, A:F.502, A:F.502 LMT.11: 7 residues within 4Å: Chain A: P.441, W.443, L.501, G.505, I.506, Y.509 Ligands: LMT.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.443 Hydrogen bonds: A:W.443, A:Y.509 LMT.12: 11 residues within 4Å: Chain A: R.21, W.22, L.36, F.37, G.40, M.435, S.436, I.504, L.511, P.537 Ligands: LDA.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.36, A:F.37, A:F.37, A:I.504, A:L.511 Hydrogen bonds: A:R.21 LMT.13: 7 residues within 4Å: Chain A: Q.58, H.59, Y.64, A.74, Y.494, F.497 Ligands: LDA.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.497 Hydrogen bonds: A:Y.64, A:Y.64 Water bridges: A:A.74 LMT.14: 7 residues within 4Å: Chain A: M.451, I.454, N.487, I.491, Y.494, A.498 Ligands: LDA.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.454, A:A.498 Hydrogen bonds: A:N.487 LMT.15: 7 residues within 4Å: Chain A: F.369, L.374, F.377, F.381, F.453 Chain B: L.82, I.86 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.369, A:L.374, A:F.377, A:F.381, A:F.453, B:L.82, B:I.86 LMT.16: 10 residues within 4Å: Chain A: L.342, M.345, T.346, V.349 Chain B: V.115, L.118, V.119, G.122, A.123, L.126 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.115, B:L.118, B:L.126, A:L.342, A:V.349 LMT.17: 6 residues within 4Å: Chain A: M.24, T.26, R.129, L.130, N.132, L.133 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.130, A:L.133, A:L.133 Hydrogen bonds: A:M.24 LMT.26: 6 residues within 4Å: Chain B: L.126, P.127, F.130, R.131, E.134 Ligands: LDA.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.131, B:R.131, B:E.134 LMT.27: 8 residues within 4Å: Chain A: F.461, Y.484, W.485 Chain B: N.44, G.45, M.47 Ligands: LDA.6, LDA.24 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.45 Hydrophobic interactions: A:F.461, A:F.461, A:W.485 LMT.28: 10 residues within 4Å: Chain A: F.356, A.360, W.363 Chain B: F.77, L.81, F.100, H.102, N.103, W.110 Ligands: LDA.23 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.77, B:L.81, B:F.100, B:F.100, B:W.110, A:F.356, A:A.360, A:W.363 Hydrogen bonds: B:H.102, B:N.103 LMT.29: 10 residues within 4Å: Chain B: W.62, L.116, V.119, A.120, F.124, I.128 Chain D: E.27, N.28, Y.30 Ligands: LDA.25 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:L.116, B:V.119, B:F.124, B:F.124 Hydrogen bonds: B:R.131, D:E.27, D:N.28, D:N.28, D:N.28

1 x PER: PEROXIDE ION(Non-covalent)

PER.18: 6 residues within 4Å: Chain A: H.276, V.279, H.325, H.326 Ligands: HEA.2, CU.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Durr, K.L. et al., A d-pathway mutation decouples the paracoccusdenitrificans cytochrome C oxidase by altering the side-chain orientation of a distant conserved glutamate. J.Mol.Biol. (2008)

Release Date

2008-09-30

Peptides

Cytochrome c oxidase subunit 1-beta: A
Cytochrome c oxidase subunit 2: B
FV fragment Chain H: C
FV fragment Chain L: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

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

Cytochrome c oxidase subunit 2

FV fragment Chain H

FV fragment Chain L

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