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1UMK
Asym. Unit
Info
Asym.Unit (65 KB)
Biol.Unit 1 (61 KB)
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(1)
Title
:
THE STRUCTURE OF HUMAN ERYTHROCYTE NADH-CYTOCHROME B5 REDUCTASE
Authors
:
S. Bando, T. Takano, T. Yubisui, K. Shirabe, M. Takeshita, C. Horii, A. Nakagawa
Date
:
03 Oct 03 (Deposition) - 02 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Flavoprotein, Beta Barrel, Fad-Binding Domain, Nadh-Binding Domain, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Bando, T. Takano, T. Yubisui, K. Shirabe, M. Takeshita, A. Nakagawa
Structure Of Human Erythrocyte Nadh-Cytochrome B5 Reductase.
Acta Crystallogr. , Sect. D V. 60 1929 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:91 , PRO A:92 , TYR A:93 , THR A:94 , VAL A:108 , ILE A:109 , LYS A:110 , TYR A:112 , PHE A:113 , PHE A:120 , GLY A:123 , GLY A:124 , LYS A:125 , MET A:126 , SER A:127 , THR A:181 , THR A:184 , HOH A:1419 , HOH A:1422 , HOH A:1438 , HOH A:1520 , HOH A:1708 , HOH A:1709 , HOH A:1710 , HOH A:1711 , HOH A:1790 , HOH A:1804 , HOH A:1805 , HOH A:2023
BINDING SITE FOR RESIDUE FAD A 1301
[
close Site info
]
SAPs(SNPs)/Variants
(11, 11)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_004619 (R57Q, chain A, )
02: VAR_018419 (S65P, chain A, )
03: VAR_010750 (L72P, chain A, )
04: VAR_004620 (V105M, chain A, )
05: VAR_010751 (T116S, chain A, )
06: VAR_004621 (S127P, chain A, )
07: VAR_004622 (L148P, chain A, )
08: VAR_010752 (A178V, chain A, )
09: VAR_010753 (C203R, chain A, )
10: VAR_010754 (C203Y, chain A, )
11: VAR_037316 (G291D, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_004619
R
58
Q
NB5R3_HUMAN
Disease (METHB-CYB5R3)
---
A
R
57
Q
02
UniProt
VAR_018419
S
66
P
NB5R3_HUMAN
Polymorphism
1130706
A
S
65
P
03
UniProt
VAR_010750
L
73
P
NB5R3_HUMAN
Disease (METHB-CYB5R3)
---
A
L
72
P
04
UniProt
VAR_004620
V
106
M
NB5R3_HUMAN
Disease (METHB-CYB5R3)
121965009
A
V
105
M
05
UniProt
VAR_010751
T
117
S
NB5R3_HUMAN
Polymorphism
1800457
A
T
116
S
06
UniProt
VAR_004621
S
128
P
NB5R3_HUMAN
Disease (METHB-CYB5R3)
---
A
S
127
P
07
UniProt
VAR_004622
L
149
P
NB5R3_HUMAN
Disease (METHB-CYB5R3)
---
A
L
148
P
08
UniProt
VAR_010752
A
179
V
NB5R3_HUMAN
Disease (METHB-CYB5R3)
201232518
A
A
178
V
09
UniProt
VAR_010753
C
204
R
NB5R3_HUMAN
Disease (METHB-CYB5R3)
---
A
C
203
R
10
UniProt
VAR_010754
C
204
Y
NB5R3_HUMAN
Disease (METHB-CYB5R3)
---
A
C
203
Y
11
UniProt
VAR_037316
G
292
D
NB5R3_HUMAN
Disease (METHB-CYB5R3)
---
A
G
291
D
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: FAD_FR (A:39-151)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FAD_FR
PS51384
Ferredoxin reductase-type FAD binding domain profile.
NB5R3_HUMAN
40-152
1
A:39-151
[
close PROSITE info
]
Exons
(8, 8)
Info
All Exons
Exon 1.3b (A:30-50)
Exon 1.4b (A:51-75)
Exon 1.4d (A:75-110)
Exon 1.5 (A:111-154)
Exon 1.6b (A:154-182)
Exon 1.7 (A:182-210)
Exon 1.8 (A:211-244)
Exon 1.9f (A:244-300)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.3b
2: Boundary 1.3b/1.4b
3: Boundary 1.4b/1.4d
4: Boundary 1.4d/1.5
5: Boundary 1.5/1.6b
6: Boundary 1.6b/1.7
7: Boundary 1.7/1.8
8: Boundary 1.8/1.9f
9: Boundary 1.9f/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000352397
1a
ENSE00001892790
chr22:
43045574-43045301
274
NB5R3_HUMAN
1-7
7
0
-
-
1.3b
ENST00000352397
3b
ENSE00001651348
chr22:
43032852-43032721
132
NB5R3_HUMAN
8-51
44
1
A:30-50
21
1.4b
ENST00000352397
4b
ENSE00000656632
chr22:
43027456-43027384
73
NB5R3_HUMAN
52-76
25
1
A:51-75
25
1.4d
ENST00000352397
4d
ENSE00001785090
chr22:
43026994-43026888
107
NB5R3_HUMAN
76-111
36
1
A:75-110
36
1.5
ENST00000352397
5
ENSE00001676775
chr22:
43024287-43024158
130
NB5R3_HUMAN
112-155
44
1
A:111-154
44
1.6b
ENST00000352397
6b
ENSE00001804814
chr22:
43023694-43023611
84
NB5R3_HUMAN
155-183
29
1
A:154-182
29
1.7
ENST00000352397
7
ENSE00001725986
chr22:
43023395-43023310
86
NB5R3_HUMAN
183-211
29
1
A:182-210
29
1.8
ENST00000352397
8
ENSE00001695409
chr22:
43019894-43019795
100
NB5R3_HUMAN
212-245
34
1
A:211-244
34
1.9f
ENST00000352397
9f
ENSE00000880579
chr22:
43015951-43014814
1138
NB5R3_HUMAN
245-301
57
1
A:244-300
57
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1umka1 (A:30-153)
2a: SCOP_d1umka2 (A:154-300)
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
Riboflavin synthase domain-like
(130)
Family
:
Ferredoxin reductase FAD-binding domain-like
(72)
Protein domain
:
cytochrome b5 reductase
(11)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1umka1
A:30-153
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ferredoxin reductase-like, C-terminal NADP-linked domain
(120)
Superfamily
:
Ferredoxin reductase-like, C-terminal NADP-linked domain
(120)
Family
:
Reductases
(68)
Protein domain
:
cytochrome b5 reductase
(11)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1umka2
A:154-300
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1umkA02 (A:146-299)
2a: CATH_1umkA01 (A:31-145)
View:
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Classes
(
)
(
)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
(85)
Human (Homo sapiens)
(1)
1a
1umkA02
A:146-299
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Elongation Factor Tu (Ef-tu); domain 3
(323)
Homologous Superfamily
:
Translation factors
(223)
Human (Homo sapiens)
(2)
2a
1umkA01
A:31-145
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_FAD_binding_6_1umkA01 (A:43-150)
2a: PFAM_NAD_binding_1_1umkA02 (A:176-284)
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Organisms
(
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(
)
Clan
:
FAD_Lum_binding
(30)
Family
:
FAD_binding_6
(24)
Homo sapiens (Human)
(1)
1a
FAD_binding_6-1umkA01
A:43-150
Clan
:
NAD_Ferredoxin
(30)
Family
:
NAD_binding_1
(30)
Homo sapiens (Human)
(2)
2a
NAD_binding_1-1umkA02
A:176-284
[
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]
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