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1KDG
Asym. Unit
Info
Asym.Unit (388 KB)
Biol.Unit 1 (381 KB)
Biol.Unit 2, α-C (1.1 MB)
Biol.Unit 2 (1.1 MB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE FLAVIN DOMAIN OF CELLOBIOSE DEHYDROGENASE
Authors
:
B. M. Hallberg, G. Henriksson, G. Pettersson, C. Divne
Date
:
13 Nov 01 (Deposition) - 13 Nov 02 (Release) - 09 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (3x)
Keywords
:
Gmc Oxidoreductase, Phbh Fold, Alpha/Beta Structure, Rossmann Fold, 6-Hydroxylated Fad, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. M. Hallberg, G. Henriksson, G. Pettersson, C. Divne
Crystal Structure Of The Flavoprotein Domain Of The Extracellular Flavocytochrome Cellobiose Dehydrogenase
J. Mol. Biol. V. 315 421 2002
[
close entry info
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Hetero Components
(6, 22)
Info
All Hetero Components
1a: 6-HYDROXY-FLAVIN-ADENINE DINUCLEOT... (6FAa)
1b: 6-HYDROXY-FLAVIN-ADENINE DINUCLEOT... (6FAb)
2a: 2-(ETHYLMERCURI-THIO)-BENZOIC ACID (EMTa)
3a: MERCURY (II) ION (HGa)
3b: MERCURY (II) ION (HGb)
3c: MERCURY (II) ION (HGc)
3d: MERCURY (II) ION (HGd)
3e: MERCURY (II) ION (HGe)
3f: MERCURY (II) ION (HGf)
3g: MERCURY (II) ION (HGg)
3h: MERCURY (II) ION (HGh)
3i: MERCURY (II) ION (HGi)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6a: UNKNOWN ATOM OR ION (UNXa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6FA
2
Ligand/Ion
6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE
2
EMT
1
Ligand/Ion
2-(ETHYLMERCURI-THIO)-BENZOIC ACID
3
HG
9
Ligand/Ion
MERCURY (II) ION
4
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
UNX
1
Ligand/Ion
UNKNOWN ATOM OR ION
[
close Hetero Component info
]
Sites
(22, 22)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:434 , MET A:512 , ASN A:513 , ARG A:617 , GLY A:618 , HOH A:1129 , HOH A:1161
BINDING SITE FOR RESIDUE NAG A 802
02
AC2
SOFTWARE
ASN A:593 , SER A:595 , ASP A:668 , THR A:670 , GLN A:671 , ALA A:679 , HOH A:1094 , HOH A:1130 , HOH A:1276 , HOH A:1283 , HOH A:1295 , HOH A:1338 , HOH A:1344 , HOH A:2108
BINDING SITE FOR RESIDUE NAG A 803
03
AC3
SOFTWARE
PRO A:527 , ASN A:599 , GLN A:602
BINDING SITE FOR RESIDUE NAG A 804
04
AC4
SOFTWARE
THR A:215 , LYS A:241 , HOH A:1306
BINDING SITE FOR RESIDUE MAN A 805
05
AC5
SOFTWARE
ASN B:593 , ASP B:668 , THR B:670 , GLN B:671 , ALA B:679 , HOH B:3094 , HOH B:3276 , HOH B:3283 , HOH B:3338 , HOH B:3344
BINDING SITE FOR RESIDUE NAG B 803
06
AC6
SOFTWARE
PRO B:527 , ASN B:599 , GLN B:602 , HOH B:3313 , HOH B:4078 , HOH B:4080
BINDING SITE FOR RESIDUE NAG B 804
07
AC7
SOFTWARE
THR B:211 , VAL B:212 , LEU B:359 , GLN B:361 , ASP B:530 , ARG B:543 , ASP B:546 , HOH B:3162 , HOH B:4033 , HOH B:4063 , HOH B:4068
BINDING SITE FOR RESIDUE MAN B 805
08
AC8
SOFTWARE
SER B:213 , ALA B:214 , THR B:215 , PRO B:216 , HOH B:4093
BINDING SITE FOR RESIDUE MAN B 806
09
AC9
SOFTWARE
THR B:215 , LYS B:241 , GLN B:356 , HOH B:3173 , HOH B:3306 , HOH B:4004 , HOH B:4031
BINDING SITE FOR RESIDUE MAN B 807
10
BC1
SOFTWARE
ASN A:317 , ASN A:385
BINDING SITE FOR RESIDUE HG A 901
11
BC2
SOFTWARE
PHE B:288
BINDING SITE FOR RESIDUE HG A 902
12
BC3
SOFTWARE
THR A:265 , SER A:266 , HOH A:2004 , SER B:266 , HOH B:3251
BINDING SITE FOR RESIDUE HG A 903
13
BC4
SOFTWARE
HG A:906 , EMT A:6907
BINDING SITE FOR RESIDUE HG A 904
14
BC5
SOFTWARE
EMT A:6907
BINDING SITE FOR RESIDUE HG A 905
15
BC6
SOFTWARE
HG A:904
BINDING SITE FOR RESIDUE HG A 906
16
BC7
SOFTWARE
ASN B:317 , ASN B:385
BINDING SITE FOR RESIDUE HG B 901
17
BC8
SOFTWARE
PHE A:288
BINDING SITE FOR RESIDUE HG B 902
18
BC9
SOFTWARE
GLY B:754 , PRO B:755 , HOH B:3069
BINDING SITE FOR RESIDUE HG B 903
19
CC1
SOFTWARE
VAL A:222 , GLY A:223 , GLY A:225 , PRO A:226 , GLY A:227 , GLU A:246 , ARG A:247 , GLY A:299 , CYS A:300 , LEU A:301 , GLY A:304 , GLY A:305 , ASN A:309 , GLY A:310 , ALA A:311 , LEU A:312 , VAL A:426 , MET A:427 , VAL A:428 , SER A:465 , ALA A:466 , GLY A:467 , ILE A:474 , ASN A:688 , HIS A:689 , ASP A:721 , ALA A:722 , ASN A:732 , PRO A:733 , GLN A:734 , LEU A:737 , HOH A:1001 , HOH A:1003 , HOH A:1006 , HOH A:1007 , HOH A:1009 , HOH A:1033 , HOH A:1035 , HOH A:1056 , HOH A:1074 , HOH A:1214 , HOH A:1351 , HOH A:2138
BINDING SITE FOR RESIDUE 6FA A 6801
20
CC2
SOFTWARE
VAL B:222 , GLY B:223 , GLY B:225 , PRO B:226 , GLY B:227 , GLU B:246 , ARG B:247 , GLY B:299 , CYS B:300 , LEU B:301 , GLY B:304 , GLY B:305 , ASN B:309 , GLY B:310 , ALA B:311 , LEU B:312 , VAL B:426 , MET B:427 , VAL B:428 , SER B:465 , ALA B:466 , GLY B:467 , ILE B:474 , ASN B:688 , HIS B:689 , ASP B:721 , ALA B:722 , ASN B:732 , PRO B:733 , GLN B:734 , LEU B:737 , HOH B:3001 , HOH B:3003 , HOH B:3006 , HOH B:3007 , HOH B:3033 , HOH B:3035 , HOH B:3056 , HOH B:3074 , HOH B:3214 , HOH B:3351
BINDING SITE FOR RESIDUE 6FA B 7801
21
CC3
SOFTWARE
ILE A:506 , ASN A:507 , GLY A:713 , HG A:904 , HG A:905 , HOH A:1117
BINDING SITE FOR RESIDUE EMT A 6907
22
CC4
SOFTWARE
PHE A:288 , LYS A:292 , PHE B:288 , LYS B:292
BINDING SITE FOR RESIDUE UNX B 904
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: GMC_OXRED_1 (A:299-322,B:299-322)
2: GMC_OXRED_2 (A:467-481,B:467-481)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GMC_OXRED_1
PS00623
GMC oxidoreductases signature 1.
CDH_PHACH
317-340
2
A:299-322
B:299-322
2
GMC_OXRED_2
PS00624
GMC oxidoreductases signature 2.
CDH_PHACH
485-499
2
A:467-481
B:467-481
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1kdga2 (A:513-693)
1b: SCOP_d1kdgb2 (B:513-693)
2a: SCOP_d1kdga1 (A:215-512,A:694-755)
2b: SCOP_d1kdgb1 (B:210-512,B:694-755)
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Classes
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)
(
)
Folds
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(
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Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FAD-linked reductases, C-terminal domain
(181)
Superfamily
:
FAD-linked reductases, C-terminal domain
(181)
Family
:
GMC oxidoreductases
(30)
Protein domain
:
Flavoprotein domain of flavocytochrome cellobiose dehydrogenase (CDH), substrate-binding domain
(2)
Basidomycetes fungus (Phanerochaete chrysosporium) [TaxId: 5306]
(2)
1a
d1kdga2
A:513-693
1b
d1kdgb2
B:513-693
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
FAD-linked reductases, N-terminal domain
(156)
Protein domain
:
Flavoprotein domain of flavocytochrome cellobiose dehydrogenase (CDH), FAD-binding domain
(2)
Basidomycetes fungus (Phanerochaete chrysosporium) [TaxId: 5306]
(2)
2a
d1kdga1
A:215-512,A:694-755
2b
d1kdgb1
B:210-512,B:694-755
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1kdgA02 (A:346-400,A:519-616,A:634-684)
1b: CATH_1kdgB02 (B:346-400,B:519-616,B:634-684)
2a: CATH_1kdgA01 (A:215-345,A:401-518,A:617-633,A:685-755)
2b: CATH_1kdgB01 (B:215-345,B:401-518,B:617-633,B:685-755)
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Architectures
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Cholesterol Oxidase; domain 2
(20)
Homologous Superfamily
:
Cholesterol Oxidase; domain 2
(20)
Phanerochaete chrysosporium. Organism_taxid: 5306. Strain: k3.
(1)
1a
1kdgA02
A:346-400,A:519-616,A:634-684
1b
1kdgB02
B:346-400,B:519-616,B:634-684
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Phanerochaete chrysosporium. Organism_taxid: 5306. Strain: k3.
(1)
2a
1kdgA01
A:215-345,A:401-518,A:617-633,A:685-755
2b
1kdgB01
B:215-345,B:401-518,B:617-633,B:685-755
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_GMC_oxred_N_1kdgB01 (B:217-499)
1b: PFAM_GMC_oxred_N_1kdgB02 (B:217-499)
2a: PFAM_GMC_oxred_C_1kdgB03 (B:615-744)
2b: PFAM_GMC_oxred_C_1kdgB04 (B:615-744)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
GMC_oxred_N
(8)
Phanerochaete chrysosporium (White-rot fungus) (Sporotrichum pruinosum)
(2)
1a
GMC_oxred_N-1kdgB01
B:217-499
1b
GMC_oxred_N-1kdgB02
B:217-499
Clan
:
no clan defined [family: GMC_oxred_C]
(22)
Family
:
GMC_oxred_C
(22)
Phanerochaete chrysosporium (White-rot fungus) (Sporotrichum pruinosum)
(2)
2a
GMC_oxred_C-1kdgB03
B:615-744
2b
GMC_oxred_C-1kdgB04
B:615-744
[
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]
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