SMTL ID : 3wg7.1 (1 other biounit)

A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

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

Ligands

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

HEA.1: 37 residues within 4Å: Chain A: A.24, G.27, M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, V.70, I.73, G.125, W.126, Y.371, F.377, H.378, L.381, S.382, V.386, I.389, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, S.461, V.465, M.468 39 PLIP interactions: 39 interactions with chain A, Hydrophobic interactions: A:A.24, A:I.37, A:R.38, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:I.73, A:F.377, A:F.377, A:L.381, A:L.381, A:V.386, A:V.386, A:I.389, A:F.393, A:F.393, A:T.424, A:F.425, 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 Water bridges: A:R.438, A:R.438, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:F.377 Metal complexes: A:H.61, A:H.378 HEA.2: 34 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, V.320, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.34, P.69, I.72, L.73 Ligands: PER.6 32 PLIP interactions: 28 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:T.309, A:T.316, A:V.320, A:F.348, A:I.356, A:I.356, A:L.358, A:V.373, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, B:I.34, B:P.69, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:H.291, A:T.316, A:D.369, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 Metal complexes: A:H.376

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

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: PER.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.198, A:H.368, A:D.369, H2O.1, H2O.11, H2O.11

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

NA.5: 4 residues within 4Å: Chain A: E.40, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.441 Water bridges: A:Q.43 NA.13: 3 residues within 4Å: Chain C: H.148, H.232, E.236 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.236, C:E.236

1 x PER: PEROXIDE ION(Non-covalent)

PER.6: 6 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP)

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

PGV.7: 25 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, F.148, H.151 Chain C: H.9, V.11, G.20, A.24, M.27, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, S.89, F.93 Ligands: PEK.14, PGV.15 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:F.148, C:A.24, C:T.28, C:W.57, C:W.57, C:W.57, C:W.58, C:F.93 Hydrogen bonds: A:R.96, A:M.97 Salt bridges: A:R.96 PGV.8: 15 residues within 4Å: Chain A: N.406, T.408, W.409, R.480 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: P.5, P.12, Q.15, A.16, L.19, S.20 15 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D, 3 interactions with chain M, 4 interactions with chain K Hydrophobic interactions: A:T.408, A:W.409, A:W.409, D:T.80, D:A.84, D:F.87, D:F.87, M:A.16, M:L.19, K:F.9, K:F.9, K:F.9 Hydrogen bonds: A:T.408 Water bridges: M:A.6 Salt bridges: K:H.10 PGV.15: 26 residues within 4Å: Chain C: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, F.86, E.90, H.207, I.209, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.7, CDL.16 30 PLIP interactions: 28 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.86, C:F.86, C:I.209, C:I.210, C:I.210, C:F.214, C:F.214, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234 Water bridges: C:S.65, C:R.221, C:H.231, C:H.231, F:Q.12, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.20: 9 residues within 4Å: Chain A: F.237 Chain C: V.91, T.95, W.99, Y.102, H.103, A.107 Chain H: N.24 Ligands: CHD.18 7 PLIP interactions: 3 interactions with chain C, 3 interactions with chain H, 1 interactions with chain A Hydrophobic interactions: C:V.91, C:W.99, C:W.99, A:F.237 Water bridges: H:N.22, H:N.24, H:N.24

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.9: 17 residues within 4Å: Chain A: F.346, V.350, Y.379, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, L.28, V.31, F.32, S.35, S.36, L.39 Chain I: R.43 16 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: A:F.346, A:V.350, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, B:V.31, B:F.32, B:F.32, B:L.39 Water bridges: B:G.8, B:F.9 Salt bridges: B:H.24, I:R.43 TGL.21: 21 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, F.414, A.415, F.418, V.419 Chain B: I.42, L.46, T.47, T.48, K.49 Chain D: R.73, S.74, T.75, E.77, W.78, V.81 Chain I: R.16, H.20 11 PLIP interactions: 6 interactions with chain A, 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:W.334, A:L.342, A:F.418, A:F.418, A:V.419, D:V.81, D:V.81, B:K.49 Salt bridges: A:K.411 Hydrogen bonds: D:T.75, D:W.78 TGL.27: 25 residues within 4Å: Chain A: T.17, L.18, L.20, L.21, F.22, W.25, W.81, F.102, L.113, F.393, F.400, S.401, I.472 Chain L: N.10, I.11, P.12, F.13, S.14, R.20, M.24, M.25, L.27, F.28, F.29, S.31 22 PLIP interactions: 14 interactions with chain A, 8 interactions with chain L Hydrophobic interactions: A:L.20, A:L.21, A:F.22, A:F.22, A:W.25, A:W.25, A:W.25, A:W.25, A:W.81, A:F.102, A:L.113, A:F.393, A:F.400, A:I.472, L:I.11, L:P.12, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29, L:F.29

1 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.10: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.196, B:E.198, B:C.200, B:C.200, B:H.204

5 x CHD: CHOLIC ACID(Non-covalent)

CHD.11: 7 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.59, B:E.62, B:T.63 Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275 CHD.17: 6 residues within 4Å: Chain C: R.156, L.160, F.164, F.219, L.223 Chain J: F.1 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:L.160, C:F.164, C:F.164, C:F.164, C:F.219, C:L.223 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.18: 8 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 Ligands: PGV.20 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, C:W.99 Hydrogen bonds: A:T.301, C:W.99 Salt bridges: A:H.233, C:H.103 CHD.25: 6 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.19 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:F.18, G:F.18, G:F.21 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 CHD.26: 6 residues within 4Å: Chain A: I.3, L.7 Chain J: Y.32, R.33, M.36, T.37 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain J Hydrophobic interactions: A:I.3, J:R.33, J:M.36, J:T.37

1 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)

PSC.12: 18 residues within 4Å: Chain A: F.268, F.321, A.325, H.328 Chain B: I.41, H.52, M.56, D.57, E.60, V.61, W.65, L.68 Chain E: H.5, D.8, F.11, L.41 Chain I: R.10, L.17 17 PLIP interactions: 3 interactions with chain E, 8 interactions with chain B, 4 interactions with chain A, 2 interactions with chain I Salt bridges: E:H.5, E:D.8 pi-Cation interactions: E:F.11 Hydrophobic interactions: B:I.41, B:M.56, B:V.61, B:W.65, B:L.68, A:F.268, A:F.321, A:A.325, A:H.328, I:L.17, I:L.17 Hydrogen bonds: B:D.57 Water bridges: B:E.60, B:E.60

3 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.14: 22 residues within 4Å: Chain A: V.155, A.203, T.207, L.215 Chain C: W.34, A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.7 18 PLIP interactions: 8 interactions with chain C, 4 interactions with chain A, 6 interactions with chain G Hydrophobic interactions: C:W.34, C:A.178, C:I.188, C:F.203, C:F.203, A:V.155, A:A.203, A:L.215, A:L.215, G:F.69 Hydrogen bonds: C:Y.181, C:A.184, C:I.188, G:T.68, G:F.70, G:N.76 Water bridges: G:F.69, G:F.69 PEK.19: 16 residues within 4Å: Chain C: K.157, H.158, Q.161, I.165, T.168, Y.172 Chain F: A.1 Chain G: K.5, R.17, F.21, G.22, L.23, L.25, P.26 Ligands: CDL.23, CHD.25 13 PLIP interactions: 7 interactions with chain G, 6 interactions with chain C Hydrophobic interactions: G:F.21, G:F.21, G:L.23, G:L.25, G:P.26, C:I.165, C:Y.172 Hydrogen bonds: G:R.17, C:K.157, C:K.157 Salt bridges: G:R.17 Water bridges: C:Q.161, C:Q.161 PEK.24: 6 residues within 4Å: Chain G: S.2, A.3, K.5, G.6, H.8 Ligands: CDL.23 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:A.3, G:K.5, G:K.5 Water bridges: G:G.9

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.16: 22 residues within 4Å: Chain C: T.48, M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, T.174, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, L.31 Ligands: PGV.15 27 PLIP interactions: 26 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:T.48, C:L.52, C:M.54, C:Y.55, C:Y.55, C:Y.55, C:Y.55, C:W.58, C:W.58, C:R.59, C:R.59, C:T.174, C:T.213, C:I.216, C:I.216, C:V.217, C:F.220, C:F.220, J:L.31 Hydrogen bonds: C:Y.55, C:R.59 Water bridges: C:R.59, C:R.59 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226 CDL.23: 17 residues within 4Å: Chain C: N.125, L.127, L.131, S.135, L.138, V.142, V.254 Chain G: L.19, L.23, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: PEK.19, PEK.24 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain G Hydrophobic interactions: C:L.131, C:L.138, C:V.254, G:L.19, G:L.23, G:L.23, G:L.30, G:L.30, G:L.37 Hydrogen bonds: C:N.125, G:N.34 Salt bridges: G:H.38, G:H.38

1 x ZN: ZINC ION(Non-covalent)

ZN.22: 4 residues within 4Å: Chain F: C.60, C.62, C.82, C.85 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.60, F:C.62, F:C.82, F:C.85

1 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.28: 11 residues within 4Å: Chain A: F.459 Chain D: W.98, Y.102 Chain L: F.37 Chain M: L.27, L.28, G.31, W.32, L.34, Y.35, H.36 5 PLIP interactions: 1 interactions with chain M, 2 interactions with chain D, 1 interactions with chain L, 1 interactions with chain A Hydrophobic interactions: M:L.34, D:W.98, D:W.98, L:F.37, A:F.459

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirata, K. et al., Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL. Nat.Methods (2014)

Release Date

2014-04-30

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 8B, mitochondrial: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

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 8B, mitochondrial

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