RCSB Protein Data Bank

Bovine heart cytochrome c oxidase in the fully oxidized state with pH 7.3 at 1.77 angstrom resolution

NOTE: Use your mouse to access Jsmol features and to drag, rotate, and zoom in and out of the structure.Help

loadScript /js/jsmol/j2s/core/package.js

loadScript /js/jsmol/j2s/core/corejmol.z.js

loadScript /js/jsmol/j2s/J/translation/PO.js

loadScript /js/jsmol/j2s/core/corescript.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__56435603914725__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript true

AppletRegistry.checkIn(jmolApplet0__56435603914725__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://www.rcsb.org/3d-view/jsmol/5XDQ","platform":"J.awtjs2d.Platform","allowjavascript":true,"fullName":"jmolApplet0__56435603914725__","codePath":"https:/js/jsmol/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"56435603914725","bgcolor":"#FFFFFF" }

setting document base to "https://www.rcsb.org/3d-view/jsmol/5XDQ"

Jmol Version: 14.31.4 2020-09-06 18:16

java.vendor: Java2Script (HTML5)

java.version: 2019-06-08 00:17:46 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #FFFFFF

backgroundColor = "#FFFFFF"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

StatusManager callback set for APPLETREADYCallback f=Jmol._readyCallback cb=APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__56435603914725__ ready

script 1 started

antialiasDisplay = true

loadScript /js/jsmol/j2s/core/corescriptcmd.z.js

FileManager.getAtomSetCollectionFromFile(https://files.rcsb.org/download/5xdq.cif)

FileManager opening url https://files.rcsb.org/download/5xdq.cif

The Resolver thinks MMCif

loadScript /js/jsmol/j2s/J/adapter/readers/cif/MMCifReader.js

loadScript /js/jsmol/j2s/J/adapter/readers/cif/CifReader.js

loadScript /js/jsmol/j2s/JU/CifDataParser.js

loadScript /js/jsmol/j2s/core/corebio.z.js

filtering with ;BIOMOLECULE 1;

TITLE: Structure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent.

Setting space group name to HM:P 21 21 21

CDL = CARDIOLIPIN

CHD = CHOLIC ACID

CU = COPPER (II) ION

CUA = DINUCLEAR COPPER ION

DMU = DECYL-BETA-D-MALTOPYRANOSIDE

EDO = 1,2-ETHANEDIOL

FME = N-FORMYLMETHIONINE

HEA = HEME-A

HOH = WATER

MG = MAGNESIUM ION

NA = SODIUM ION

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

PER = PEROXIDE ION

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

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

SAC = N-ACETYL-SERINE

TGL = TRISTEAROYLGLYCEROL

TPO = PHOSPHOTHREONINE

ZN = ZINC ION

noncrystallographic symmetry operator 1 null

noncrystallographic symmetry operator 2 null

noncrystallographic symmetry operator 3 null

noncrystallographic symmetry operator 4 null

noncrystallographic symmetry operator 5 null

noncrystallographic symmetry operator 6 null

noncrystallographic symmetry operator 7 null

noncrystallographic symmetry operator 8 null

noncrystallographic symmetry operator 9 null

noncrystallographic symmetry operator 10 null

noncrystallographic symmetry operator 11 null

noncrystallographic symmetry operator 12 null

noncrystallographic symmetry operator 13 null

noncrystallographic symmetry operator 14 null

noncrystallographic symmetry operator 15 null

noncrystallographic symmetry operator 16 null

noncrystallographic symmetry operator 17 null

noncrystallographic symmetry operator 18 null

noncrystallographic symmetry operator 19 null

noncrystallographic symmetry operator 20 null

noncrystallographic symmetry operator 21 null

noncrystallographic symmetry operator 22 null

noncrystallographic symmetry operator 23 null

noncrystallographic symmetry operator 24 null

noncrystallographic symmetry operator 25 null

noncrystallographic symmetry operator 26 null

5XDQ

biomolecule 1 operators 1 ASYM_IDs A,B,C,D,E,F,G,H,I,J,K,L,M,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,KE,LE,ME,NE,OE,PE,QE,RE,SE,TE,UE,VE,WE

found biomolecule 1: A,B,C,D,E,F,G,H,I,J,K,L,M,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,KE,LE,ME,NE,OE,PE,QE,RE,SE,TE,UE,VE,WE

biomolecule 2 operators 1 ASYM_IDs N,O,P,Q,R,S,T,U,V,W,X,Y,Z,JC,KC,LC,MC,NC,OC,PC,QC,RC,SC,TC,UC,VC,WC,XC,YC,ZC,AD,BD,CD,DD,ED,FD,GD,HD,ID,JD,KD,LD,MD,ND,OD,PD,QD,RD,SD,TD,UD,VD,WD,XD,YD,ZD,AE,BE,CE,DE,EE,FE,GE,HE,IE,JE,XE,YE,ZE,AF,BF,CF,DF,EF,FF,GF,HF,IF,JF

found biomolecule 2: N,O,P,Q,R,S,T,U,V,W,X,Y,Z,JC,KC,LC,MC,NC,OC,PC,QC,RC,SC,TC,UC,VC,WC,XC,YC,ZC,AD,BD,CD,DD,ED,FD,GD,HD,ID,JD,KD,LD,MD,ND,OD,PD,QD,RD,SD,TD,UD,VD,WD,XD,YD,ZD,AE,BE,CE,DE,EE,FE,GE,HE,IE,JE,XE,YE,ZE,AF,BF,CF,DF,EF,FF,GF,HF,IF,JF

739 bonds added

loadScript /js/jsmol/j2s/core/coresym.z.js

loadScript /js/jsmol/j2s/JU/Tensor.js

loadScript /js/jsmol/j2s/JU/Eigen.js

loadScript /js/jsmol/j2s/javajs/api/EigenInterface.js

loadScript /js/jsmol/j2s/JU/EigenSort.js

Time for openFile(https://files.rcsb.org/download/5xdq.cif): 4900 ms

reading 17343 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

model 1.1 alternative locations: AB

Default Van der Waals type for model set to Jmol

17343 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 428 ms

TITLE: Structure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent.

CDL = CARDIOLIPIN

CHD = CHOLIC ACID

CU = COPPER (II) ION

CUA = DINUCLEAR COPPER ION

DMU = DECYL-BETA-D-MALTOPYRANOSIDE

EDO = 1,2-ETHANEDIOL

FME = N-FORMYLMETHIONINE

HEA = HEME-A

HOH = WATER

MG = MAGNESIUM ION

NA = SODIUM ION

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

PER = PEROXIDE ION

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

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

SAC = N-ACETYL-SERINE

TGL = TRISTEAROYLGLYCEROL

TPO = PHOSPHOTHREONINE

ZN = ZINC ION

5XDQ

739 bonds added

loadScript /js/jsmol/j2s/core/corescriptmath.z.js

loadScript /js/jsmol/j2s/J/bspt/PointIterator.js

Script completed

Jmol script terminated

script 2 started

0 atoms hidden

17343 atoms selected

1312 atoms selected

2 atoms selected

1 atoms selected

17343 atoms selected

Script completed

Jmol script terminated

script 3 started

0 atoms hidden

17343 atoms selected

defaultColorScheme = "jmol"

1312 atoms selected

17343 atoms selected

Script completed

Jmol script terminated

script 4 started

Script completed

Jmol script terminated

loadScript /js/jsmol/j2s/J/g3d/HermiteRenderer.js

Input - Custom Scripting

History

Structure Details

Select Options

Style

Color

Surface

Surface options may take a long time to render, especially for larger structures

Select a different viewer

Help Links

Jmol, an open source Java viewer for chemical structures in 3D (http://www.jmol.org)

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left:-5px; } 5XDQ | pdb_00005xdq

Bovine heart cytochrome c oxidase in the fully oxidized state with pH 7.3 at 1.77 angstrom resolution

Scripting Options

Structure Details

Select Options

Help Links

5XDQ | pdb_00005xdq