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1XFD
Biol. Unit 2
Info
Asym.Unit (503 KB)
Biol.Unit 1 (250 KB)
Biol.Unit 2 (249 KB)
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(1)
Title
:
STRUCTURE OF A HUMAN A-TYPE POTASSIUM CHANNEL ACCELERATING FACTOR DPPX, A MEMBER OF THE DIPEPTIDYL AMINOPEPTIDASE FAMILY
Authors
:
P. Strop, A. J. Bankovich, K. C. Hansen, K. C. Garcia, A. T. Brunger
Date
:
14 Sep 04 (Deposition) - 26 Oct 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Dppx; Dpp6; Kv4; Kv; Kaf, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Strop, A. J. Bankovich, K. C. Hansen, K. C. Garcia, A. T. Brunger
Structure Of A Human A-Type Potassium Channel Interacting Protein Dppx, A Member Of The Dipeptidyl Aminopeptidase Family
J. Mol. Biol. V. 343 1055 2004
[
close entry info
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Hetero Components
(4, 29)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
1e: BETA-D-MANNOSE (BMAe)
1f: BETA-D-MANNOSE (BMAf)
1g: BETA-D-MANNOSE (BMAg)
1h: BETA-D-MANNOSE (BMAh)
1i: BETA-D-MANNOSE (BMAi)
1j: BETA-D-MANNOSE (BMAj)
1k: BETA-D-MANNOSE (BMAk)
1l: BETA-D-MANNOSE (BMAl)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
2d: ALPHA-D-MANNOSE (MANd)
2e: ALPHA-D-MANNOSE (MANe)
2f: ALPHA-D-MANNOSE (MANf)
2g: ALPHA-D-MANNOSE (MANg)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
3t: N-ACETYL-D-GLUCOSAMINE (NAGt)
3u: N-ACETYL-D-GLUCOSAMINE (NAGu)
3v: N-ACETYL-D-GLUCOSAMINE (NAGv)
3w: N-ACETYL-D-GLUCOSAMINE (NAGw)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
4b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
4c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
4d: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGd)
4e: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGe)
4f: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGf)
4g: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGg)
4h: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGh)
4i: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGi)
4j: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGj)
4k: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGk)
4l: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGl)
4m: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGm)
4n: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGn)
4o: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGo)
4p: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGp)
4q: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGq)
4r: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGr)
4s: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGs)
4t: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGt)
4u: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGu)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
5
Ligand/Ion
BETA-D-MANNOSE
2
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
10
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(30, 30)
Info
All Sites
01: AC2 (SOFTWARE)
02: DC8 (SOFTWARE)
03: DC9 (SOFTWARE)
04: EC1 (SOFTWARE)
05: EC2 (SOFTWARE)
06: EC3 (SOFTWARE)
07: EC4 (SOFTWARE)
08: EC5 (SOFTWARE)
09: EC6 (SOFTWARE)
10: EC7 (SOFTWARE)
11: EC8 (SOFTWARE)
12: EC9 (SOFTWARE)
13: FC1 (SOFTWARE)
14: FC2 (SOFTWARE)
15: FC3 (SOFTWARE)
16: FC4 (SOFTWARE)
17: FC5 (SOFTWARE)
18: FC6 (SOFTWARE)
19: FC7 (SOFTWARE)
20: FC8 (SOFTWARE)
21: FC9 (SOFTWARE)
22: GC1 (SOFTWARE)
23: GC2 (SOFTWARE)
24: GC3 (SOFTWARE)
25: GC4 (SOFTWARE)
26: GC5 (SOFTWARE)
27: GC6 (SOFTWARE)
28: GC7 (SOFTWARE)
29: GC8 (SOFTWARE)
30: GC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
NDG A:1319 , BMA A:3319 , GLN D:699
BINDING SITE FOR RESIDUE NAG A 2319
02
DC8
SOFTWARE
ILE C:284 , ASN C:319 , SER C:321 , NAG C:2319
BINDING SITE FOR RESIDUE NDG C 1319
03
DC9
SOFTWARE
NDG C:1319 , BMA C:3319
BINDING SITE FOR RESIDUE NAG C 2319
04
EC1
SOFTWARE
NAG C:2319
BINDING SITE FOR RESIDUE BMA C 3319
05
EC2
SOFTWARE
TRP C:168 , ASN C:173 , MET C:573 , ARG C:765 , NDG C:2173
BINDING SITE FOR RESIDUE NDG C 1173
06
EC3
SOFTWARE
ASP C:575 , NDG C:1173 , MAN C:3173
BINDING SITE FOR RESIDUE NDG C 2173
07
EC4
SOFTWARE
NDG C:2173
BINDING SITE FOR RESIDUE MAN C 3173
08
EC5
SOFTWARE
ASN C:404 , SER C:426 , GLU C:427 , NAG C:2404
BINDING SITE FOR RESIDUE NDG C 1404
09
EC6
SOFTWARE
NDG C:1404
BINDING SITE FOR RESIDUE NAG C 2404
10
EC7
SOFTWARE
GLU C:780 , LYS C:811 , ASN C:813 , NAG C:2813 , ASN D:841 , GLU D:845
BINDING SITE FOR RESIDUE NAG C 1813
11
EC8
SOFTWARE
NAG C:1813 , BMA C:3813
BINDING SITE FOR RESIDUE NAG C 2813
12
EC9
SOFTWARE
NAG C:2813
BINDING SITE FOR RESIDUE BMA C 3813
13
FC1
SOFTWARE
ASN C:535 , LYS C:583 , NAG C:2535
BINDING SITE FOR RESIDUE NDG C 1535
14
FC2
SOFTWARE
ASN C:587 , NDG C:1535
BINDING SITE FOR RESIDUE NAG C 2535
15
FC3
SOFTWARE
ILE D:284 , ASN D:319 , SER D:321 , NAG D:2319
BINDING SITE FOR RESIDUE NDG D 1319
16
FC4
SOFTWARE
NDG D:1319 , BMA D:3319
BINDING SITE FOR RESIDUE NAG D 2319
17
FC5
SOFTWARE
THR A:619 , NAG D:2319
BINDING SITE FOR RESIDUE BMA D 3319
18
FC6
SOFTWARE
TRP D:168 , ASN D:173 , MET D:573 , NDG D:2173
BINDING SITE FOR RESIDUE NDG D 1173
19
FC7
SOFTWARE
ASP D:575 , GLU D:727 , NDG D:1173 , MAN D:3173
BINDING SITE FOR RESIDUE NDG D 2173
20
FC8
SOFTWARE
GLU D:727 , ASN D:728 , NDG D:2173
BINDING SITE FOR RESIDUE MAN D 3173
21
FC9
SOFTWARE
ASN D:404 , SER D:426 , GLU D:427 , NAG D:2404
BINDING SITE FOR RESIDUE NDG D 1404
22
GC1
SOFTWARE
NDG D:1404 , MAN D:3404
BINDING SITE FOR RESIDUE NAG D 2404
23
GC2
SOFTWARE
NAG D:2404 , MAN D:4404
BINDING SITE FOR RESIDUE MAN D 3404
24
GC3
SOFTWARE
LEU D:762 , MAN D:3404
BINDING SITE FOR RESIDUE MAN D 4404
25
GC4
SOFTWARE
ASN C:841 , GLU C:845 , GLU D:780 , LYS D:811 , ASN D:813 , NAG D:2813
BINDING SITE FOR RESIDUE NAG D 1813
26
GC5
SOFTWARE
NAG D:1813 , BMA D:3813
BINDING SITE FOR RESIDUE NAG D 2813
27
GC6
SOFTWARE
NAG D:2813
BINDING SITE FOR RESIDUE BMA D 3813
28
GC7
SOFTWARE
ASN D:535 , LYS D:583 , NAG D:2535
BINDING SITE FOR RESIDUE NDG D 1535
29
GC8
SOFTWARE
ASN D:587 , NDG D:1535 , BMA D:3535
BINDING SITE FOR RESIDUE NAG D 2535
30
GC9
SOFTWARE
LYS D:128 , NAG D:2535
BINDING SITE FOR RESIDUE BMA D 3535
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_073680 (M385L, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_073680
M
385
L
DPP6_HUMAN
Disease (MRD33)
786205143
C/D
M
385
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1xfda1 (A:127-591)
1b: SCOP_d1xfdb1 (B:127-591)
1c: SCOP_d1xfdc1 (C:127-591)
1d: SCOP_d1xfdd1 (D:127-591)
2a: SCOP_d1xfda2 (A:592-849)
2b: SCOP_d1xfdb2 (B:592-849)
2c: SCOP_d1xfdc2 (C:592-849)
2d: SCOP_d1xfdd2 (D:592-849)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
8-bladed beta-propeller
(135)
Superfamily
:
DPP6 N-terminal domain-like
(99)
Family
:
DPP6 N-terminal domain-like
(99)
Protein domain
:
Dipeptidyl aminopeptidase-like protein 6, DPP6, N-terminal domain
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1xfda1
A:127-591
1b
d1xfdb1
B:127-591
1c
d1xfdc1
C:127-591
1d
d1xfdd1
D:127-591
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
alpha/beta-Hydrolases
(971)
Superfamily
:
alpha/beta-Hydrolases
(971)
Family
:
DPP6 catalytic domain-like
(63)
Protein domain
:
Dipeptidyl aminopeptidase-like protein 6, DPP6, C-terminal domain
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1xfda2
A:592-849
2b
d1xfdb2
B:592-849
2c
d1xfdc2
C:592-849
2d
d1xfdd2
D:592-849
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1xfdA02 (A:591-849)
1b: CATH_1xfdB02 (B:591-849)
1c: CATH_1xfdC02 (C:591-849)
1d: CATH_1xfdD02 (D:591-849)
2a: CATH_1xfdA01 (A:127-590)
2b: CATH_1xfdB01 (B:127-590)
2c: CATH_1xfdC01 (C:127-590)
2d: CATH_1xfdD01 (D:127-590)
View:
Select:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1820, no name defined]
(692)
Human (Homo sapiens)
(118)
1a
1xfdA02
A:591-849
1b
1xfdB02
B:591-849
1c
1xfdC02
C:591-849
1d
1xfdD02
D:591-849
Class
:
Mainly Beta
(13760)
Architecture
:
8 Propellor
(110)
Topology
:
Methanol Dehydrogenase; Chain A
(110)
Homologous Superfamily
:
[code=2.140.10.30, no name defined]
(74)
Human (Homo sapiens)
(59)
2a
1xfdA01
A:127-590
2b
1xfdB01
B:127-590
2c
1xfdC01
C:127-590
2d
1xfdD01
D:127-590
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Peptidase_S9_1xfdD01 (D:641-849)
1b: PFAM_Peptidase_S9_1xfdD02 (D:641-849)
1c: PFAM_Peptidase_S9_1xfdD03 (D:641-849)
1d: PFAM_Peptidase_S9_1xfdD04 (D:641-849)
2a: PFAM_DPPIV_N_1xfdD05 (D:195-561)
2b: PFAM_DPPIV_N_1xfdD06 (D:195-561)
2c: PFAM_DPPIV_N_1xfdD07 (D:195-561)
2d: PFAM_DPPIV_N_1xfdD08 (D:195-561)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
AB_hydrolase
(347)
Family
:
Peptidase_S9
(57)
Homo sapiens (Human)
(33)
1a
Peptidase_S9-1xfdD01
D:641-849
1b
Peptidase_S9-1xfdD02
D:641-849
1c
Peptidase_S9-1xfdD03
D:641-849
1d
Peptidase_S9-1xfdD04
D:641-849
Clan
:
Beta_propeller
(192)
Family
:
DPPIV_N
(38)
Homo sapiens (Human)
(33)
2a
DPPIV_N-1xfdD05
D:195-561
2b
DPPIV_N-1xfdD06
D:195-561
2c
DPPIV_N-1xfdD07
D:195-561
2d
DPPIV_N-1xfdD08
D:195-561
[
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]
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