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.
5B1B
Biol. Unit 2
Info
Asym.Unit (1.4 MB)
Biol.Unit 1 (694 KB)
Biol.Unit 2 (693 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
BOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY REDUCED STATE AT 1.6 ANGSTROM RESOLUTION
Authors
:
N. Yano, K. Muramoto, A. Shimada, S. Takemura, J. Baba, H. Fujisawa, M. M K. Shinzawa-Itoh, E. Yamashita, T. Tsukihara, S. Yoshikawa
Date
:
01 Dec 15 (Deposition) - 14 Sep 16 (Release) - 23 Nov 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
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, Proton Pump, Heme
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Yano, K. Muramoto, A. Shimada, S. Takemura, J. Baba, H. Fujisawa, M. Mochizuki, K. Shinzawa-Itoh, E. Yamashita, T. Tsukihara, S. Yoshikawa
The Mg2+-Containing Water Cluster Of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents In Each Catalytic Cycle.
J. Biol. Chem. V. 291 23882 2016
[
close entry info
]
Hetero Components
(13, 26)
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)
02g: CHOLIC ACID (CHDg)
02h: CHOLIC ACID (CHDh)
04a: DINUCLEAR COPPER ION (CUAa)
04b: DINUCLEAR COPPER ION (CUAb)
03a: COPPER (II) ION (CUa)
04b: COPPER (II) ION (CUb)
05a: DECYL-BETA-D-MALTOPYRANOSIDE (DMUa)
05b: DECYL-BETA-D-MALTOPYRANOSIDE (DMUb)
05c: DECYL-BETA-D-MALTOPYRANOSIDE (DMUc)
05d: DECYL-BETA-D-MALTOPYRANOSIDE (DMUd)
06a: N-FORMYLMETHIONINE (FMEa)
06b: N-FORMYLMETHIONINE (FMEb)
06c: N-FORMYLMETHIONINE (FMEc)
06d: N-FORMYLMETHIONINE (FMEd)
07a: HEME-A (HEAa)
07b: HEME-A (HEAb)
07c: HEME-A (HEAc)
07d: HEME-A (HEAd)
08a: MAGNESIUM ION (MGa)
08b: MAGNESIUM ION (MGb)
09a: SODIUM ION (NAa)
09b: SODIUM ION (NAb)
10a: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKa)
10b: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKb)
10c: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKc)
10d: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKd)
10e: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKe)
10f: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKf)
11a: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVa)
11b: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVb)
11c: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVc)
11d: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVd)
11e: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVe)
11f: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVf)
11g: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVg)
11h: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVh)
12a: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIME... (PSCa)
12b: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIME... (PSCb)
13a: N-ACETYL-SERINE (SACa)
13b: N-ACETYL-SERINE (SACb)
14a: TRISTEAROYLGLYCEROL (TGLa)
14b: TRISTEAROYLGLYCEROL (TGLb)
14c: TRISTEAROYLGLYCEROL (TGLc)
14d: TRISTEAROYLGLYCEROL (TGLd)
14e: TRISTEAROYLGLYCEROL (TGLe)
14f: TRISTEAROYLGLYCEROL (TGLf)
15a: PHOSPHOTHREONINE (TPOa)
15b: PHOSPHOTHREONINE (TPOb)
16a: UNKNOWN ATOM OR ION (UNXa)
16b: UNKNOWN ATOM OR ION (UNXb)
17a: ZINC ION (ZNa)
17b: 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
DMU
2
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
6
FME
2
Mod. Amino Acid
N-FORMYLMETHIONINE
7
HEA
2
Ligand/Ion
HEME-A
8
MG
-1
Ligand/Ion
MAGNESIUM ION
9
NA
-1
Ligand/Ion
SODIUM ION
10
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
11
PGV
4
Ligand/Ion
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
12
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
13
SAC
1
Mod. Amino Acid
N-ACETYL-SERINE
14
TGL
3
Ligand/Ion
TRISTEAROYLGLYCEROL
15
TPO
1
Mod. Amino Acid
PHOSPHOTHREONINE
16
UNX
1
Ligand/Ion
UNKNOWN ATOM OR ION
17
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(33, 33)
Info
All Sites
01: AD1 (SOFTWARE)
02: AD8 (SOFTWARE)
03: AD9 (SOFTWARE)
04: AE1 (SOFTWARE)
05: AE4 (SOFTWARE)
06: AE5 (SOFTWARE)
07: AE6 (SOFTWARE)
08: AF1 (SOFTWARE)
09: AF2 (SOFTWARE)
10: AF3 (SOFTWARE)
11: AF4 (SOFTWARE)
12: AF5 (SOFTWARE)
13: AF6 (SOFTWARE)
14: AF7 (SOFTWARE)
15: AF8 (SOFTWARE)
16: AF9 (SOFTWARE)
17: AG1 (SOFTWARE)
18: AG2 (SOFTWARE)
19: AG3 (SOFTWARE)
20: AG4 (SOFTWARE)
21: AG5 (SOFTWARE)
22: AG6 (SOFTWARE)
23: AG7 (SOFTWARE)
24: AG8 (SOFTWARE)
25: AG9 (SOFTWARE)
26: AH1 (SOFTWARE)
27: AH2 (SOFTWARE)
28: AH3 (SOFTWARE)
29: AH4 (SOFTWARE)
30: AH5 (SOFTWARE)
31: AH6 (SOFTWARE)
32: AH7 (SOFTWARE)
33: AH8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AD1
SOFTWARE
MET A:271 , TRP A:275 , GLN B:59 , GLU B:62 , THR B:63 , HOH B:445 , HOH B:446 , HOH B:457 , ARG T:14 , ARG T:17 , PHE T:21 , GLY T:22 , PEK T:103
binding site for residue CHD B 303
02
AD8
SOFTWARE
HIS A:233 , ASP A:300 , THR A:301 , TYR A:304 , HOH A:716 , TRP C:99 , HIS C:103 , HOH C:446 , HOH C:463 , HOH C:493 , HOH C:513 , HOH C:523 , HOH C:533 , LEU P:127
binding site for residue CHD C 307
03
AD9
SOFTWARE
LYS C:157 , HIS C:158 , GLN C:161 , ALA F:1 , ARG G:17 , PHE G:21 , CDL G:101 , CHD G:103 , ILE N:311 , GLN O:59
binding site for residue PEK C 308
04
AE1
SOFTWARE
THR C:95 , TRP C:99 , TYR C:102 , HIS C:103 , LEU C:106 , ALA C:107 , HOH C:448 , HOH C:466 , HOH C:495 , HOH C:512 , ASN H:24 , ALA T:1
binding site for residue PGV C 309
05
AE4
SOFTWARE
ASN C:125 , LEU C:127 , LEU C:131 , PEK C:308 , HOH C:481 , TPO G:11 , SER G:27 , LEU G:30 , CYS G:31 , ASN G:34 , LEU G:37 , HIS G:38 , HOH G:216 , HOH G:258 , HOH G:267 , HOH G:271 , PHE N:282 , ILE N:286 , ASP N:300 , SER N:307 , ILE N:311 , LEU O:78 , LEU O:81
binding site for residue CDL G 101
06
AE5
SOFTWARE
SER G:2 , ALA G:3 , LYS G:5 , GLY G:6 , HIS G:8 , HOH G:246 , HOH G:259 , HOH G:270 , LYS P:77 , ARG P:80 , ILE P:84 , VAL P:91 , THR P:95 , PHE P:98 , TRP P:240 , VAL P:247
binding site for residue PEK G 102
07
AE6
SOFTWARE
PEK C:308 , ARG G:14 , ARG G:17 , PHE G:18 , PHE G:21 , GLY G:22 , HOH G:206 , HOH G:220 , HOH G:236 , MET N:271 , GLN O:59 , GLU O:62 , THR O:63 , HOH O:417
binding site for residue CHD G 103
08
AF1
SOFTWARE
THR N:31 , SER N:34 , ILE N:37 , ARG N:38 , TYR N:54 , VAL N:58 , HIS N:61 , ALA N:62 , MET N:65 , VAL N:70 , ILE N:73 , GLY N:125 , TRP N:126 , TYR N:371 , PHE N:377 , HIS N:378 , SER N:382 , PHE N:393 , MET N:417 , PHE N:425 , GLN N:428 , ARG N:438 , ARG N:439 , VAL N:465 , HOH N:724 , HOH N:738 , HOH N:787
binding site for residue HEA N 601
09
AF2
SOFTWARE
TRP N:126 , TRP N:236 , VAL N:243 , TYR N:244 , ILE N:247 , HIS N:290 , HIS N:291 , THR N:309 , ILE N:312 , THR N:316 , GLY N:317 , GLY N:352 , GLY N:355 , ILE N:356 , LEU N:358 , ALA N:359 , ASP N:364 , HIS N:368 , VAL N:373 , HIS N:376 , PHE N:377 , VAL N:380 , LEU N:381 , ARG N:438 , HOH N:708 , HOH N:776 , HOH N:807 , HOH N:821
binding site for residue HEA N 602
10
AF3
SOFTWARE
HIS N:240 , HIS N:290 , HIS N:291
binding site for residue CU N 603
11
AF4
SOFTWARE
HIS N:368 , ASP N:369 , GLU O:198 , HOH O:436 , HOH O:448 , HOH O:540
binding site for residue MG N 604
12
AF5
SOFTWARE
GLU N:40 , GLY N:45 , SER N:441 , HOH N:888
binding site for residue NA N 605
13
AF6
SOFTWARE
ASN N:406 , THR N:408 , TRP N:409 , HOH N:750 , HOH N:907 , PHE Q:87 , PHE X:9 , PRO Z:12 , GLN Z:15 , ALA Z:16 , LEU Z:19 , SER Z:20 , HOH Z:209
binding site for residue PGV N 606
14
AF7
SOFTWARE
PHE N:94 , PRO N:95 , ARG N:96 , MET N:97 , HOH N:735 , HOH N:757 , HIS P:9 , GLY P:20 , ALA P:24 , ASN P:50 , TRP P:57 , TRP P:58 , GLU P:64 , HIS P:71 , GLY P:82 , PEK T:101
binding site for residue PGV N 607
15
AF8
SOFTWARE
ASN N:422 , PHE N:426 , PHE N:430 , LEU N:433 , HOH N:905 , LEU O:7 , LEU O:28 , PHE O:32 , SER O:35 , LEU O:39 , ARG V:43 , HOH V:157
binding site for residue TGL N 608
16
AF9
SOFTWARE
THR N:17 , LEU N:18 , TRP N:25 , TRP N:81 , LEU N:113 , PHE N:400 , PRO Y:12 , PHE Y:13 , SER Y:14 , ARG Y:20 , MET Y:24 , PHE Y:28 , PHE Y:29 , SER Y:31 , HOH Y:125
binding site for residue TGL N 609
17
AG1
SOFTWARE
HIS O:161 , CYS O:196 , GLU O:198 , CYS O:200 , HIS O:204 , MET O:207
binding site for residue CUA O 301
18
AG2
SOFTWARE
ALA G:1 , TRP P:99 , HIS P:103 , ALA P:107 , CHD P:307 , HOH P:403 , HOH P:418 , HOH P:461 , HOH P:470 , HOH P:536 , HOH P:545 , ASN U:24
binding site for residue PGV P 301
19
AG3
SOFTWARE
LEU N:110 , SER P:29 , MET P:33 , PHE P:37 , HOH P:402 , TYR W:48 , CYS W:49 , TRP W:52
binding site for residue DMU P 302
20
AG4
SOFTWARE
MET P:54 , TRP P:58 , VAL P:61 , SER P:65 , THR P:66 , ILE P:210 , PHE P:214 , ARG P:221 , HIS P:226 , PHE P:227 , THR P:228 , HIS P:231 , HIS P:232 , PHE P:233 , GLY P:234 , CDL P:305 , HOH P:428 , HOH P:444 , HOH P:455 , HOH P:490
binding site for residue PGV P 304
21
AG5
SOFTWARE
MET P:51 , LEU P:52 , TYR P:55 , ARG P:59 , ILE P:62 , ARG P:63 , PHE P:67 , PHE P:220 , LYS P:224 , HIS P:226 , PGV P:304 , HOH P:410 , HOH P:459 , HOH P:472 , HOH P:495 , HOH P:499 , LYS W:8
binding site for residue CDL P 305
22
AG6
SOFTWARE
ARG P:156 , PHE P:164 , PHE P:219 , LEU P:223 , HOH P:551 , PHE W:1
binding site for residue CHD P 306
23
AG7
SOFTWARE
HIS N:233 , ASP N:300 , THR N:301 , TYR N:304 , HOH N:736 , TRP P:99 , HIS P:103 , PGV P:301 , HOH P:424 , HOH P:486 , HOH P:506
binding site for residue CHD P 307
24
AG8
SOFTWARE
TRP N:334 , PHE N:414 , HOH N:891 , LEU O:39 , THR O:47 , HOH O:567 , ARG Q:73 , THR Q:75 , GLU Q:77 , TRP Q:78 , MET Q:86 , HOH Q:363 , ARG V:16 , HOH V:151
binding site for residue TGL Q 201
25
AG9
SOFTWARE
PHE N:321 , HIS N:328 , ILE O:41 , HIS O:52 , MET O:56 , ASP O:57 , VAL O:61 , HOH O:422 , GLU R:6 , THR R:7 , ASP R:8 , ARG V:10
binding site for residue PSC R 201
26
AH1
SOFTWARE
CYS S:60 , CYS S:62 , CYS S:82 , CYS S:85
binding site for residue ZN S 101
27
AH2
SOFTWARE
HIS N:151 , PGV N:607 , TRP P:34 , TYR P:181 , TYR P:182 , ALA P:184 , PHE P:186 , THR P:187 , ILE P:188 , PHE P:198 , GLY P:202 , TRP T:62 , THR T:68 , PHE T:69 , PHE T:70 , HIS T:71 , ASN T:76 , HOH T:203 , HOH T:242
binding site for residue PEK T 101
28
AH3
SOFTWARE
LYS C:77 , ARG C:80 , ILE C:84 , VAL C:91 , PHE C:98 , TRP C:240 , VAL C:247 , SER T:2 , ALA T:3 , LYS T:5 , GLY T:6 , HIS T:8 , TPO T:11 , HOH T:221
binding site for residue PEK T 102
29
AH4
SOFTWARE
SER A:279 , ILE A:311 , CHD B:303 , LYS P:157 , HIS P:158 , GLN P:161 , THR P:168 , TYR P:172 , ALA S:1 , ARG T:17 , GLY T:22 , CDL T:104 , HOH T:206
binding site for residue PEK T 103
30
AH5
SOFTWARE
ILE A:286 , ASP A:300 , SER A:307 , ILE A:311 , ALA B:77 , LEU B:78 , LEU B:81 , TYR B:85 , HOH C:446 , ASN P:125 , LEU P:127 , SER P:135 , TYR P:253 , SER T:27 , LEU T:30 , CYS T:31 , ASN T:34 , LEU T:37 , HIS T:38 , PEK T:103 , HOH T:223 , HOH T:250
binding site for residue CDL T 104
31
AH6
SOFTWARE
ILE N:3 , PHE N:8 , TYR W:32 , ARG W:33 , THR W:37
binding site for residue CHD W 101
32
AH7
SOFTWARE
TRP Q:98 , LEU Z:27 , LEU Z:28 , GLY Z:31 , TRP Z:32 , TYR Z:35 , HIS Z:36 , HOH Z:208 , HOH Z:217
binding site for residue DMU Z 101
33
AH8
SOFTWARE
TRP N:236 , PHE N:238 , GLY N:239 , PRO N:241 , GLU N:242 , VAL N:243 , ILE N:245 , LEU N:246 , ILE N:247 , LEU N:248 , ILE N:280 , GLY N:284 , VAL N:287 , HIS N:290 , ILE N:312 , HEA N:602 , CU N:603
binding site for Di-peptide HIS N 240 and TYR N 244
[
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 N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
Chain U
Chain V
Chain W
Chain X
Chain Y
Chain Z
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 (1.4 MB)
Header - Asym.Unit
Biol.Unit 1 (694 KB)
Header - Biol.Unit 1
Biol.Unit 2 (693 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
5B1B
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help