PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
3X2Q
Biol. Unit 1
Info
Asym.Unit (1.3 MB)
Biol.Unit 1 (662 KB)
Biol.Unit 2 (669 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF CYANIDE-BOUND BOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY OXIDIZED STATE AT 2.0 ANGSTROM RESOLUTION
Authors
:
N. Yano, K. Muramoto, M. Mochizuki, K. Shinzawa-Itoh, E. Yamashita, S. Yoshikawa, T. Tsukihara
Date
:
26 Dec 14 (Deposition) - 10 Jun 15 (Release) - 10 Jun 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M (1x)
Biol. Unit 2: N,O,P,Q,R,S,T,U,V,W,X,Y,Z (1x)
Keywords
:
Oxidoreductase, Respiratory Chain, Electron Transport, Heme, Iron, Mitochondorial Inner Membrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Yano, K. Muramoto, M. Mochizuki, K. Shinzawa-Itoh, E. Yamashita, S. Yoshikawa, T. Tsukihara
X-Ray Structure Of Cyanide-Bound Bovine Heart Cytochrome C Oxidase In The Fully Oxidized State At 2. 0 A Resolution.
Acta Crystallogr. , Sect. F V. 71 726 2015
[
close entry info
]
Hetero Components
(14, 27)
Info
All Hetero Components
01a: CARDIOLIPIN (CDLa)
01b: CARDIOLIPIN (CDLb)
01c: CARDIOLIPIN (CDLc)
01d: CARDIOLIPIN (CDLd)
02a: CHOLIC ACID (CHDa)
02b: CHOLIC ACID (CHDb)
02c: CHOLIC ACID (CHDc)
02d: CHOLIC ACID (CHDd)
02e: CHOLIC ACID (CHDe)
02f: CHOLIC ACID (CHDf)
04a: DINUCLEAR COPPER ION (CUAa)
04b: DINUCLEAR COPPER ION (CUAb)
03a: COPPER (II) ION (CUa)
04b: COPPER (II) ION (CUb)
05a: CYANIDE ION (CYNa)
05b: CYANIDE ION (CYNb)
06a: DECYL-BETA-D-MALTOPYRANOSIDE (DMUa)
06b: DECYL-BETA-D-MALTOPYRANOSIDE (DMUb)
06c: DECYL-BETA-D-MALTOPYRANOSIDE (DMUc)
06d: DECYL-BETA-D-MALTOPYRANOSIDE (DMUd)
07a: N-FORMYLMETHIONINE (FMEa)
07b: N-FORMYLMETHIONINE (FMEb)
07c: N-FORMYLMETHIONINE (FMEc)
07d: N-FORMYLMETHIONINE (FMEd)
08a: HEME-A (HEAa)
08b: HEME-A (HEAb)
08c: HEME-A (HEAc)
08d: HEME-A (HEAd)
09a: MAGNESIUM ION (MGa)
09b: MAGNESIUM ION (MGb)
10a: SODIUM ION (NAa)
10b: SODIUM ION (NAb)
11a: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKa)
11b: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKb)
11c: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKc)
11d: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKd)
11e: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKe)
11f: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKf)
12a: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVa)
12b: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVb)
12c: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVc)
12d: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVd)
12e: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVe)
12f: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVf)
12g: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVg)
12h: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVh)
13a: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIME... (PSCa)
13b: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIME... (PSCb)
14a: N-ACETYL-SERINE (SACa)
14b: N-ACETYL-SERINE (SACb)
15a: TRISTEAROYLGLYCEROL (TGLa)
15b: TRISTEAROYLGLYCEROL (TGLb)
15c: TRISTEAROYLGLYCEROL (TGLc)
15d: TRISTEAROYLGLYCEROL (TGLd)
15e: TRISTEAROYLGLYCEROL (TGLe)
15f: TRISTEAROYLGLYCEROL (TGLf)
16a: PHOSPHOTHREONINE (TPOa)
16b: PHOSPHOTHREONINE (TPOb)
17a: UNKNOWN ATOM OR ION (UNXa)
17b: UNKNOWN ATOM OR ION (UNXb)
18a: ZINC ION (ZNa)
18b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CDL
2
Ligand/Ion
CARDIOLIPIN
2
CHD
3
Ligand/Ion
CHOLIC ACID
3
CU
-1
Ligand/Ion
COPPER (II) ION
4
CUA
1
Ligand/Ion
DINUCLEAR COPPER ION
5
CYN
1
Ligand/Ion
CYANIDE ION
6
DMU
2
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
7
FME
2
Mod. Amino Acid
N-FORMYLMETHIONINE
8
HEA
2
Ligand/Ion
HEME-A
9
MG
-1
Ligand/Ion
MAGNESIUM ION
10
NA
-1
Ligand/Ion
SODIUM ION
11
PEK
3
Ligand/Ion
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
12
PGV
4
Ligand/Ion
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
13
PSC
1
Ligand/Ion
(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
14
SAC
1
Mod. Amino Acid
N-ACETYL-SERINE
15
TGL
3
Ligand/Ion
TRISTEAROYLGLYCEROL
16
TPO
1
Mod. Amino Acid
PHOSPHOTHREONINE
17
UNX
1
Ligand/Ion
UNKNOWN ATOM OR ION
18
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(32, 32)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: EC2 (SOFTWARE)
28: EC5 (SOFTWARE)
29: FC1 (SOFTWARE)
30: FC2 (SOFTWARE)
31: FC5 (SOFTWARE)
32: FC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:240 , VAL A:243 , HIS A:290 , HIS A:291 , HEA A:603 , CU A:604
BINDING SITE FOR RESIDUE CYN A 601
02
AC2
SOFTWARE
GLY A:27 , THR A:31 , SER A:34 , ILE A:37 , ARG A:38 , TYR A:54 , VAL A:58 , HIS A:61 , ALA A:62 , MET A:65 , MET A:69 , VAL A:70 , ILE A:73 , GLY A:125 , TRP A:126 , TYR A:371 , PHE A:377 , HIS A:378 , SER A:382 , VAL A:386 , MET A:417 , PHE A:425 , GLN A:428 , ARG A:438 , ARG A:439 , SER A:458 , MET A:468 , HOH A:729 , HOH A:733 , HOH A:750
BINDING SITE FOR RESIDUE HEA A 602
03
AC3
SOFTWARE
TRP A:126 , TRP A:236 , VAL A:243 , TYR A:244 , HIS A:290 , HIS A:291 , THR A:309 , ILE A:312 , THR A:316 , GLY A:317 , GLY A:352 , GLY A:355 , ILE A:356 , LEU A:358 , ALA A:359 , ASP A:364 , HIS A:368 , VAL A:373 , HIS A:376 , PHE A:377 , VAL A:380 , LEU A:381 , ARG A:438 , CYN A:601 , HOH A:736 , HOH A:755 , HOH A:761 , HOH A:766
BINDING SITE FOR RESIDUE HEA A 603
04
AC4
SOFTWARE
HIS A:240 , HIS A:290 , HIS A:291 , CYN A:601
BINDING SITE FOR RESIDUE CU A 604
05
AC5
SOFTWARE
HIS A:368 , ASP A:369 , HOH A:760 , GLU B:198 , HOH B:429 , HOH B:430
BINDING SITE FOR RESIDUE MG A 605
06
AC6
SOFTWARE
GLU A:40 , GLN A:43 , GLY A:45 , SER A:441 , HOH A:709
BINDING SITE FOR RESIDUE NA A 606
07
AC7
SOFTWARE
TYR A:379 , ASN A:422 , PHE A:426 , HIS A:429 , PHE A:430 , LEU A:433 , LEU B:7 , GLY B:8 , LEU B:28 , PHE B:32 , SER B:35 , SER B:36
BINDING SITE FOR RESIDUE TGL A 607
08
AC8
SOFTWARE
PHE A:94 , PRO A:95 , ARG A:96 , MET A:97 , HOH A:804 , HIS C:9 , ASN C:50 , TRP C:57 , TRP C:58 , GLU C:64 , HIS C:71
BINDING SITE FOR RESIDUE PGV A 608
09
AC9
SOFTWARE
ASN A:406 , THR A:408 , TRP A:409 , HOH A:822 , PHE K:9 , HIS K:10 , GLN M:15 , ALA M:16 , LEU M:19 , SER M:20
BINDING SITE FOR RESIDUE PGV A 609
10
BC1
SOFTWARE
HIS B:161 , CYS B:196 , GLU B:198 , CYS B:200 , HIS B:204 , MET B:207
BINDING SITE FOR RESIDUE CUA B 301
11
BC2
SOFTWARE
MET A:271 , TRP A:275 , GLN B:59 , GLU B:62 , THR B:63 , THR B:66 , HOH B:466 , HOH B:476 , HOH B:516 , PEK P:309 , ARG T:14 , ARG T:17 , GLY T:22
BINDING SITE FOR RESIDUE CHD B 302
12
BC3
SOFTWARE
VAL C:61 , SER C:65 , THR C:66 , ILE C:210 , PHE C:214 , ARG C:221 , HIS C:226 , PHE C:227 , HIS C:231 , HIS C:232 , PHE C:233 , GLY C:234 , CDL C:303 , HOH C:414 , HOH C:425
BINDING SITE FOR RESIDUE PGV C 302
13
BC4
SOFTWARE
MET C:51 , LEU C:52 , TYR C:55 , TRP C:58 , ARG C:59 , ARG C:63 , PHE C:67 , THR C:213 , LYS C:224 , HIS C:226 , PGV C:302 , HOH C:477 , LYS J:8
BINDING SITE FOR RESIDUE CDL C 303
14
BC5
SOFTWARE
ARG C:156 , LEU C:160 , GLN C:161 , PHE C:164 , LEU C:223 , PHE J:1
BINDING SITE FOR RESIDUE CHD C 304
15
BC6
SOFTWARE
HIS A:233 , ASP A:300 , THR A:301 , TYR A:304 , TRP C:99 , HIS C:103 , PGV C:307 , LEU P:127 , CDL T:102
BINDING SITE FOR RESIDUE CHD C 305
16
BC7
SOFTWARE
LYS C:157 , HIS C:158 , GLN C:161 , ALA F:1 , ARG G:17 , GLY G:22 , CDL G:103 , GLN O:59 , CHD O:302 , HOH O:481
BINDING SITE FOR RESIDUE PEK C 306
17
BC8
SOFTWARE
TRP C:99 , TYR C:102 , HIS C:103 , ALA C:107 , CHD C:305
BINDING SITE FOR RESIDUE PGV C 307
18
BC9
SOFTWARE
TRP A:334 , GLY A:343 , LYS A:411 , PHE A:414 , VAL A:419 , LYS B:49 , ARG D:73 , TRP D:78 , VAL D:81 , HOH D:323 , ARG I:16
BINDING SITE FOR RESIDUE TGL D 201
19
CC1
SOFTWARE
PHE A:321 , ILE B:41 , HIS B:52 , MET B:56 , ASP B:57 , HOH B:489 , ASP E:8 , PHE E:11 , LEU E:41 , HOH E:339 , ARG I:10
BINDING SITE FOR RESIDUE PSC E 201
20
CC2
SOFTWARE
CYS F:60 , CYS F:62 , CYS F:82 , CYS F:85
BINDING SITE FOR RESIDUE ZN F 101
21
CC3
SOFTWARE
TRP C:34 , MET C:40 , TRP G:62 , GLY G:63
BINDING SITE FOR RESIDUE DMU G 101
22
CC4
SOFTWARE
HIS A:151 , TRP C:34 , TYR C:181 , TYR C:182 , ALA C:184 , PHE C:186 , THR C:187 , ILE C:188 , PHE C:198 , GLY C:202 , TRP G:62 , THR G:68 , PHE G:69 , PHE G:70 , HIS G:71 , ASN G:76 , HOH G:209
BINDING SITE FOR RESIDUE PEK G 102
23
CC5
SOFTWARE
LEU C:127 , LEU C:131 , SER C:135 , LEU C:250 , VAL C:254 , PEK C:306 , LEU G:23 , SER G:27 , LEU G:30 , CYS G:31 , ASN G:34 , HIS G:38 , PHE N:282 , ASP N:300 , SER N:307 , ILE N:311 , ALA O:77 , LEU O:78 , LEU O:81 , TYR O:85 , CHD P:308
BINDING SITE FOR RESIDUE CDL G 103
24
CC6
SOFTWARE
SER G:2 , ALA G:3 , LYS G:5 , HIS G:8 , HOH G:227 , PHE N:282 , LYS P:77 , ARG P:80 , ILE P:84 , PHE P:98 , TRP P:240
BINDING SITE FOR RESIDUE PEK G 104
25
CC7
SOFTWARE
THR A:17 , LEU A:18 , PHE A:22 , TRP A:25 , LEU A:113 , PHE A:400 , ILE L:11 , PRO L:12 , PHE L:13 , SER L:14 , ARG L:20 , MET L:24 , PHE L:29
BINDING SITE FOR RESIDUE TGL L 101
26
CC8
SOFTWARE
TRP D:98 , LEU M:28 , TRP M:32 , TYR M:35 , HIS M:36
BINDING SITE FOR RESIDUE DMU M 101
27
EC2
SOFTWARE
PEK C:306 , ARG G:14 , ARG G:17 , PHE G:21 , GLY G:22 , MET N:271 , GLU O:62 , THR O:63 , HOH O:401 , HOH O:478 , HOH O:483 , HOH O:487
BINDING SITE FOR RESIDUE CHD O 302
28
EC5
SOFTWARE
ALA G:1 , ASP N:298 , TRP P:99 , HIS P:103 , ALA P:107 , CHD P:308 , ASN U:22
BINDING SITE FOR RESIDUE PGV P 302
29
FC1
SOFTWARE
CDL G:103 , HIS N:233 , ASP N:300 , THR N:301 , TYR N:304 , TRP P:99 , HIS P:103 , PGV P:302
BINDING SITE FOR RESIDUE CHD P 308
30
FC2
SOFTWARE
SER A:279 , CHD B:302 , LYS P:157 , HIS P:158 , GLN P:161 , ILE P:165 , THR P:168 , HOH P:426 , HOH P:475 , ALA S:1 , ARG T:17 , GLY T:22 , CDL T:102
BINDING SITE FOR RESIDUE PEK P 309
31
FC5
SOFTWARE
LYS C:77 , ILE C:84 , VAL C:91 , THR C:95 , PHE C:98 , TRP C:240 , VAL C:247 , SER T:2 , ALA T:3 , LYS T:5 , GLY T:6 , HIS T:8
BINDING SITE FOR RESIDUE PEK T 101
32
FC6
SOFTWARE
ASP A:300 , SER A:307 , ILE A:311 , LEU B:78 , LEU B:81 , TYR B:85 , CHD C:305 , LEU P:127 , LEU P:131 , VAL P:142 , TRP P:258 , PEK P:309 , SER T:27 , LEU T:30 , CYS T:31 , ASN T:34 , LEU T:37 , HIS T:38 , HOH T:215
BINDING SITE FOR RESIDUE CDL T 102
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (1.3 MB)
Header - Asym.Unit
Biol.Unit 1 (662 KB)
Header - Biol.Unit 1
Biol.Unit 2 (669 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3X2Q
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help