Research workbench

Cryo-structure of the paracoccus denitrificans four-subunit cytochrome C oxidase in the completely oxidized state complexed with an antibody fv fragment

Analyse Cryo-structure of the paracoccus denitrificans four-subunit cytochrome C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QLE
Type: protein
Length: 1,333 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C oxidase polypeptide I-beta; Cytochrome C oxidase polypeptide II; Cytochrome…
EC: 1.9.3.1
UniProt: P98002, P08306, P06030, P77921
Ligands: HEA, PC1, CUA, CU, CA, MN
Pockets: 18 · best druggability 0.90

Structure

x-ray diffraction · 6 distinct chains · 49% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome C oxidase polypeptide I-beta (EC 1.9.3.1)	protein	538	65% helix, 1% strand	P98002
B	Cytochrome C oxidase polypeptide II (EC 1.9.3.1)	protein	252	33% helix, 16% strand	P08306
C	Cytochrome C oxidase polypeptide III (EC 1.9.3.1)	protein	273	68% helix, 1% strand	P06030
D	Ccytochrome C oxidase (EC 1.9.3.1)	protein	43	70% helix, 0% strand	P77921
H	Heavy chain antibody fv fragment	protein	119	5% helix, 47% strand	—
L	Light chain antibody fv fragment	protein	108	3% helix, 48% strand	—

Ligands and binding sites

HEA · Heme-A · ligand · 2 copies · chains A, B
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, B, C, D
CUA · Dinuclear copper ion · ligand · chains B
CU · Copper (II) ion · metal · chains A
CA · Calcium ion · metal · chains A
MN · Manganese (II) ion · metal · chains A, B

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

Pockets

18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1194	0.90	0.92	118	HEA
2	1122	0.83	0.83	94	PC1
3	1032	0.79	0.80	97	PC1
4	84	0.77	0.98	28	empty
5	551	0.70	0.79	68	empty

Interfaces

8 interfaces between chains.

A–B · 3930 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 2786 Å² buried · 11 hydrogen bonds · protein-protein
H–L · 947 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 819 Å² buried · 11 hydrogen bonds · protein-protein
B–L · 453 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1QLE · Cryo-structure of the paracoccus denitrificans four-subunit cytochrome C oxidase in the… · the same entry in another collection · chain L against L, TM-score 1.00
P98002 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 1-beta (P98002) · a predicted model of the same protein · chain A against A, TM-score 0.99
P08306 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 2 (P08306) · a predicted model of the same protein · chain B against A, TM-score 0.99
P06030 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 3 (P06030) · a predicted model of the same protein · chain C against A, TM-score 0.98
P77921 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 4 (P77921) · a predicted model of the same protein · chain D against A, TM-score 0.90

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 P98002
Every structure of UniProt P08306
Every structure of UniProt P06030
Every structure of UniProt P77921
Elsewhere: RCSB PDB 1QLE · PDBe 1QLE · UniProt P98002 · UniProt P08306 · UniProt P06030 · UniProt P77921

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.