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5DJQ
Biol. Unit 4
Info
Asym.Unit (1.4 MB)
Biol.Unit 1 (346 KB)
Biol.Unit 2 (355 KB)
Biol.Unit 3 (348 KB)
Biol.Unit 4 (351 KB)
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(1)
Title
:
THE STRUCTURE OF CBB3 CYTOCHROME OXIDASE.
Authors
:
S. Buschmann, E. Warkentin, H. Xie, M. Kohlstaedt, J. D. Langer, U. Erml H. Michel
Date
:
02 Sep 15 (Deposition) - 13 Jan 16 (Release) - 27 Jul 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,K,L,M,N,O,P,Q
Biol. Unit 1: A,B,C,N (1x)
Biol. Unit 2: D,E,F,O (1x)
Biol. Unit 3: G,H,I,P (1x)
Biol. Unit 4: K,L,M,Q (1x)
Keywords
:
Oxidoreductase, Cbb3-Cytochrome C Oxidase, Pseudomonas_stutzeri
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Buschmann, E. Warkentin, H. Xie, J. D. Langer, U. Ermler, H. Michel
The Structure Of Cbb3 Cytochrome Oxidase Provides Insights Into Proton Pumping.
Science V. 329 327 2010
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
2c: COPPER (II) ION (CUc)
2d: COPPER (II) ION (CUd)
3a: HEXACYANOFERRATE(3-) (FC6a)
3b: HEXACYANOFERRATE(3-) (FC6b)
3c: HEXACYANOFERRATE(3-) (FC6c)
3d: HEXACYANOFERRATE(3-) (FC6d)
4a: HEME C (HECa)
4b: HEME C (HECb)
4c: HEME C (HECc)
4d: HEME C (HECd)
4e: HEME C (HECe)
4f: HEME C (HECf)
4g: HEME C (HECg)
4h: HEME C (HECh)
4i: HEME C (HECi)
4j: HEME C (HECj)
4k: HEME C (HECk)
4l: HEME C (HECl)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
5c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
5d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
5e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
5f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
5g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
5h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
6a: HYDROGEN PEROXIDE (PEOa)
6b: HYDROGEN PEROXIDE (PEOb)
6c: HYDROGEN PEROXIDE (PEOc)
6d: HYDROGEN PEROXIDE (PEOd)
7a: PHOSPHATE ION (PO4a)
7b: PHOSPHATE ION (PO4b)
7c: PHOSPHATE ION (PO4c)
7d: PHOSPHATE ION (PO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CU
-1
Ligand/Ion
COPPER (II) ION
3
FC6
1
Ligand/Ion
HEXACYANOFERRATE(3-)
4
HEC
3
Ligand/Ion
HEME C
5
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
PEO
1
Ligand/Ion
HYDROGEN PEROXIDE
7
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(15, 15)
Info
All Sites
01: AD2 (SOFTWARE)
02: AF1 (SOFTWARE)
03: AF2 (SOFTWARE)
04: AF3 (SOFTWARE)
05: AF4 (SOFTWARE)
06: AF5 (SOFTWARE)
07: AF6 (SOFTWARE)
08: AF7 (SOFTWARE)
09: AF8 (SOFTWARE)
10: AH3 (SOFTWARE)
11: AH4 (SOFTWARE)
12: AH5 (SOFTWARE)
13: AH6 (SOFTWARE)
14: AH7 (SOFTWARE)
15: AH8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AD2
SOFTWARE
GLY C:265 , GLN C:266 , GLN C:269 , ARG C:275 , ARG M:206 , PRO M:215 , SER M:263 , LEU M:264
binding site for residue FC6 C 403
02
AF1
SOFTWARE
GLU K:122 , TYR K:123 , TRP K:203 , VAL K:210 , LEU K:214 , HIS K:257 , LEU K:279 , SER K:283 , SER K:320 , GLY K:324 , PRO K:325 , MET K:327 , ALA K:328 , ASN K:333 , HIS K:337 , THR K:342 , HIS K:345 , VAL K:346 , GLY K:349 , HEM K:502 , CU K:503 , CA K:504 , PEO K:507 , SER L:102
binding site for residue HEM K 501
03
AF2
SOFTWARE
MET K:29 , GLY K:32 , VAL K:33 , ILE K:35 , ALA K:36 , LEU K:39 , ARG K:57 , HIS K:60 , THR K:61 , VAL K:64 , ILE K:65 , GLU K:122 , TYR K:123 , ASP K:340 , ILE K:343 , VAL K:346 , HIS K:347 , ALA K:350 , LEU K:351 , TYR K:395 , ARG K:437 , GLY K:441 , PHE K:444 , HEM K:501 , CA K:504 , LYS L:103
binding site for residue HEM K 502
04
AF3
SOFTWARE
HIS K:207 , HIS K:257 , HIS K:258 , HEM K:501 , PEO K:507
binding site for residue CU K 503
05
AF4
SOFTWARE
ARG K:57 , GLU K:122 , HEM K:501 , HEM K:502 , SER L:102
binding site for residue CA K 504
06
AF5
SOFTWARE
ALA K:124 , LEU K:126 , ASP K:131 , ASN K:179
binding site for residue CA K 505
07
AF6
SOFTWARE
MET K:273 , ILE K:329 , LYS K:330 , THR K:331 , TYR M:72
binding site for residue PO4 K 506
08
AF7
SOFTWARE
HIS K:207 , VAL K:210 , HIS K:258 , HEM K:501 , CU K:503
binding site for residue PEO K 507
09
AF8
SOFTWARE
ARG C:206 , PRO C:215 , SER C:263 , LEU C:264 , GLY M:265 , GLN M:266 , GLN M:269 , ARG M:275
binding site for residue FC6 M 401
10
AH3
SOFTWARE
PHE K:53 , LEU K:427 , GLU L:63 , CYS L:65 , VAL L:66 , GLY L:67 , HIS L:69 , LYS L:103 , ARG L:104 , THR L:105 , GLY L:106 , PRO L:107 , TYR L:116 , TRP L:120 , HIS L:121 , HIS L:124 , VAL L:132 , SER L:135 , MET L:137 , PRO L:138 , TYR L:140 , MET L:188
binding site for Di-peptide HEC L 301 and CYS L 68
11
AH4
SOFTWARE
PHE K:53 , LEU K:427 , TYR L:60 , GLU L:63 , GLY L:64 , VAL L:66 , GLY L:67 , CYS L:68 , HIS L:69 , THR L:105 , GLY L:106 , PRO L:107 , TYR L:116 , TRP L:120 , HIS L:121 , HIS L:124 , VAL L:132 , SER L:135 , MET L:137 , PRO L:138 , TYR L:140 , MET L:188
binding site for Di-peptide HEC L 301 and CYS L 65
12
AH5
SOFTWARE
ARG M:166 , ILE M:183 , ALA M:184 , ALA M:185 , MET M:186 , PRO M:187 , TRP M:189 , VAL M:205 , TYR M:229 , THR M:232 , ALA M:234 , VAL M:235 , CYS M:236 , HIS M:237 , LEU M:247 , GLY M:248 , PRO M:250 , LEU M:252 , TRP M:258 , ILE M:259 , TYR M:260 , GLY M:261 , LEU M:267 , THR M:270 , ILE M:271 , GLY M:277 , HEC M:403
binding site for Di-peptide HEC M 402 and CYS M 233
13
AH6
SOFTWARE
ARG M:166 , ILE M:183 , ALA M:184 , ALA M:185 , MET M:186 , PRO M:187 , TRP M:189 , VAL M:205 , THR M:232 , CYS M:233 , ALA M:234 , VAL M:235 , HIS M:237 , GLY M:238 , MET M:244 , LEU M:247 , GLY M:248 , ALA M:249 , PRO M:250 , LEU M:252 , TRP M:258 , ILE M:259 , TYR M:260 , GLY M:261 , LEU M:267 , THR M:270 , ILE M:271 , GLY M:277 , HEC M:403
binding site for Di-peptide HEC M 402 and CYS M 236
14
AH7
SOFTWARE
TYR L:116 , TYR M:142 , CYS M:143 , SER M:144 , ILE M:145 , HIS M:147 , GLY M:148 , GLY M:156 , PHE M:157 , PRO M:158 , LEU M:160 , TRP M:165 , ARG M:166 , TRP M:167 , ILE M:174 , SER M:177 , ILE M:178 , ALA M:184 , GLY M:277 , GLN M:278 , MET M:279 , PRO M:280 , GLN M:282 , HEC M:402
binding site for Di-peptide HEC M 403 and CYS M 146
15
AH8
SOFTWARE
TYR L:116 , PHE M:139 , TYR M:142 , SER M:144 , ILE M:145 , CYS M:146 , HIS M:147 , GLY M:156 , PRO M:158 , LEU M:160 , TRP M:165 , ARG M:166 , TRP M:167 , ILE M:174 , SER M:177 , ILE M:178 , ALA M:184 , GLY M:277 , GLN M:278 , MET M:279 , PRO M:280 , GLN M:282 , HEC M:402
binding site for Di-peptide HEC M 403 and CYS M 143
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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[
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
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CATH Domains
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Pfam Domains
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Asym.Unit (1.4 MB)
Header - Asym.Unit
Biol.Unit 1 (346 KB)
Header - Biol.Unit 1
Biol.Unit 2 (355 KB)
Header - Biol.Unit 2
Biol.Unit 3 (348 KB)
Header - Biol.Unit 3
Biol.Unit 4 (351 KB)
Header - Biol.Unit 4
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