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Bovine heart cytochrome C oxidase in the carbon monoxide-bound mixed- valence state at 1.68 ångström resolution (50 K)

Analyse Bovine heart cytochrome C oxidase in the carbon monoxide-bound mixed- valence… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5B3S
Type: protein
Length: 3,550 residues
Chains: 26
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C oxidase subunit 1; Cytochrome C oxidase subunit 2; Cytochrome C oxidase…
EC: 7.1.1.9
UniProt: P00396, P68530, P00415, P00423, P00426, P00428, P07471, P00429, P04038, P07470, P13183, P00430, P10175
Ligands: CHD, PGV, TGL, PEK, HEA, CDL, CUA, PSC, CU, MG, NA, ZN, CMO, PO4
Pockets: 20 · best druggability 0.91

Structure

x-ray diffraction · 13 distinct chains · 59% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, N	Cytochrome C oxidase subunit 1 (EC 7.1.1.9)	protein	514	72% helix, 1% strand	P00396
B, O	Cytochrome C oxidase subunit 2 (EC 7.1.1.9)	protein	227	35% helix, 26% strand	P68530
C, P	Cytochrome C oxidase subunit 3 (EC 7.1.1.9)	protein	259	76% helix, 0% strand	P00415
D, Q	Cytochrome C oxidase subunit 4 isoform 1, mitochondrial	protein	144	52% helix, 3% strand	P00423
E, R	Cytochrome C oxidase subunit 5A, mitochondrial	protein	105	64% helix, 1% strand	P00426
F, S	Cytochrome C oxidase subunit 5B, mitochondrial	protein	94	16% helix, 28% strand	P00428
G, T	Cytochrome C oxidase subunit 6A2, mitochondrial	protein	84	30% helix, 2% strand	P07471
H, U	Cytochrome C oxidase subunit 6B1	protein	79	61% helix, 1% strand	P00429
I, V	Cytochrome C oxidase subunit 6C	protein	73	70% helix, 1% strand	P04038
J, W	Cytochrome C oxidase subunit 7A1, mitochondrial	protein	58	67% helix, 0% strand	P07470
K, X	Cytochrome C oxidase subunit 7B, mitochondrial	protein	49	55% helix, 0% strand	P13183
L, Y	Cytochrome C oxidase subunit 7C, mitochondrial	protein	46	59% helix, 0% strand	P00430
M, Z	Cytochrome C oxidase subunit 8B, mitochondrial	protein	43	67% helix, 2% strand	P10175

Ligands and binding sites

CHD · Cholic acid · ligand · 9 copies · chains A, C, P, G, N, O, J, W, B, T, Y, Z
PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 8 copies · chains A, D, K, M, C, F, H, P, T, G, N, U, Q, X, Z, S
TGL · Tristearoylglycerol · ligand · 6 copies · chains A, B, I, D, L, N, O, V, Q, Y
PEK · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(stearoyloxy)methyl]ethyl (5E,8E,11E,14E)-icosa-5,8, 11,14-tetraenoate · ligand · 6 copies · chains A, C, G, F, N, O, P, T, B, S
HEA · Heme-A · ligand · 4 copies · chains A, B, N, O
CDL · Cardiolipin · ligand · 4 copies · chains C, J, G, N, O, P, W, A, B, T
CUA · Dinuclear copper ion · ligand · 2 copies · chains B, O
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 · ligand · 2 copies · chains A, B, E, I, N, O, R, V
CU · Copper (II) ion · metal · 2 copies · chains A, N
MG · Magnesium ion · metal · 2 copies · chains A, B, N, O
NA · Sodium ion · metal · 2 copies · chains A, N
ZN · Zinc ion · metal · 2 copies · chains F, S
CMO · Carbon monoxide · ion · 2 copies · chains A, N
PO4 · Phosphate ion · ion · 2 copies · chains H, U
EDO · 1,2-ethanediol · additive · 94 copies · chains A, M, D, L, B, C, F, I, H, G, J, E, N, Z, Q, P, Y, S, O, V, U, W, T, R
DMU · Decyl-beta-D-maltopyranoside · additive · 23 copies · chains C, J, A, G, D, K, B, L, M, O, P, W, N, T, Q, X, Y, Z

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1102	0.91	0.93	126	HEA, CMO, EDO
2	1194	0.91	0.92	129	HEA, CMO, EDO
3	1089	0.86	0.87	87	PGV
4	1184	0.86	0.86	107	PGV, PEK
5	1010	0.83	0.84	102	EDO

Interfaces

80 interfaces between chains.

N–O · 3633 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 3619 Å² buried · 38 hydrogen bonds · protein-protein
N–P · 2644 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 2631 Å² buried · 17 hydrogen bonds · protein-protein
N–Y · 1739 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified, 4 disulfide (disulfide, formylation, acetylation, phosphorylation).

Compared structures

5B3S · Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at… · the same entry in another collection · chain K against K, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P00396
Every structure of UniProt P68530
Every structure of UniProt P00415
Every structure of UniProt P00423
Every structure of UniProt P00426
Every structure of UniProt P00428
Every structure of UniProt P07471
Every structure of UniProt P00429
Every structure of UniProt P04038
Every structure of UniProt P07470
Every structure of UniProt P13183
Every structure of UniProt P00430
Every structure of UniProt P10175
Elsewhere: RCSB PDB 5B3S · PDBe 5B3S · UniProt P00396 · UniProt P68530 · UniProt P00415 · UniProt P00423 · UniProt P00426 · UniProt P00428 · UniProt P07471 · UniProt P00429 · UniProt P04038 · UniProt P07470 · UniProt P13183 · UniProt P00430 · UniProt P10175

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