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1ZMI
Asym. Unit
Info
Asym.Unit (52 KB)
Biol.Unit 1 (25 KB)
Biol.Unit 2 (23 KB)
Biol.Unit 3 (90 KB)
Biol.Unit 4 (46 KB)
Biol.Unit 5 (46 KB)
Biol.Unit 6 (46 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN ALPHA_DEFENSIN-2 (VARIANT GLY16->D-ALA), P 32 2 1 SPACE GROUP )
Authors
:
J. Lubkowski, A. Prahl, W. Lu
Date
:
10 May 05 (Deposition) - 16 Aug 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.15
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (2x)
Biol. Unit 4: A,B,C,D (1x)
Biol. Unit 5: A,B,C,D (1x)
Biol. Unit 6: A,B,C,D (1x)
Keywords
:
Alpha-Defensin, Antimicrobial, D-Amino Acid Substitution, Antimicrobial Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Xie, A. Prahl, B. Ericksen, Z. Wu, P. Zeng, X. Li, W. Y. Lu, J. Lubkowski, W. Lu
Reconstruction Of The Conserved Beta-Bulge In Mammalian Defensins Using D-Amino Acids.
J. Biol. Chem. V. 280 32921 2005
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Hetero Components
(3, 11)
Info
All Hetero Components
1a: D-ALANINE (DALa)
1b: D-ALANINE (DALb)
1c: D-ALANINE (DALc)
1d: D-ALANINE (DALd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DAL
4
Mod. Amino Acid
D-ALANINE
2
GOL
4
Ligand/Ion
GLYCEROL
3
SO4
3
Ligand/Ion
SULFATE ION
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG B:13 , CYS B:29 , HOH B:137 , HOH B:167 , ARG C:14
BINDING SITE FOR RESIDUE SO4 B 401
2
AC2
SOFTWARE
GLY B:11 , HOH B:138 , HOH B:219 , ARG C:14 , THR C:17
BINDING SITE FOR RESIDUE SO4 B 402
3
AC3
SOFTWARE
ILE B:5 , ARG B:23 , HOH B:112 , HOH B:114 , HOH B:128 , HOH B:140 , HOH B:227 , HOH B:228
BINDING SITE FOR RESIDUE SO4 B 403
4
AC4
SOFTWARE
CYS A:3 , TRP A:25 , HOH A:102 , HOH A:106 , HOH A:186 , HOH A:203 , GOL A:507 , PHE B:27 , ILE C:5 , HOH C:150
BINDING SITE FOR RESIDUE GOL A 501
5
AC5
SOFTWARE
CYS A:1 , TYR B:2 , CYS B:3 , HOH B:153 , HOH B:178
BINDING SITE FOR RESIDUE GOL B 502
6
AC6
SOFTWARE
PRO B:6 , ARG B:14 , LEU B:24 , ALA B:26 , HOH B:206 , HOH C:113
BINDING SITE FOR RESIDUE GOL B 503
7
AC7
SOFTWARE
PRO A:6 , ALA A:7 , GOL A:501 , ILE C:5 , ARG C:23 , TRP C:25
BINDING SITE FOR RESIDUE GOL A 507
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: DEFENSIN (A:1-29,B:1-29,C:1-29,D:1-29)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DEFENSIN
PS00269
Mammalian defensins signature.
DEF3_HUMAN
66-94
4
A:1-29
B:1-29
C:1-29
D:1-29
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Exons
(1, 4)
Info
All Exons
Exon 1.3 (A:1-29 | B:1-29 | C:1-29 | D:1-29)
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All Exon Boundaries
1: Boundary 1.2/1.3
2: Boundary 1.3/-
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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
1.1
ENST00000327857
1
ENSE00001493010
chr8:
6875823-6875744
80
DEF3_HUMAN
-
0
0
-
-
1.2
ENST00000327857
2
ENSE00001719742
chr8:
6874384-6874198
187
DEF3_HUMAN
1-59
59
0
-
-
1.3
ENST00000327857
3
ENSE00001306731
chr8:
6873621-6873391
231
DEF3_HUMAN
59-94
36
4
A:1-29
B:1-29
C:1-29
D:1-29
29
29
29
29
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1zmia_ (A:)
1b: SCOP_d1zmib_ (B:)
1c: SCOP_d1zmic_ (C:)
1d: SCOP_d1zmid_ (D:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Defensin-like
(59)
Superfamily
:
Defensin-like
(59)
Family
:
Defensin
(50)
Protein domain
:
automated matches
(20)
Human (Homo sapiens) [TaxId: 9606]
(17)
1a
d1zmia_
A:
1b
d1zmib_
B:
1c
d1zmic_
C:
1d
d1zmid_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Defensin_1_1zmiD01 (D:1-29)
1b: PFAM_Defensin_1_1zmiD02 (D:1-29)
1c: PFAM_Defensin_1_1zmiD03 (D:1-29)
1d: PFAM_Defensin_1_1zmiD04 (D:1-29)
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Clan
:
Defensin
(30)
Family
:
Defensin_1
(14)
Homo sapiens (Human)
(14)
1a
Defensin_1-1zmiD01
D:1-29
1b
Defensin_1-1zmiD02
D:1-29
1c
Defensin_1-1zmiD03
D:1-29
1d
Defensin_1-1zmiD04
D:1-29
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (52 KB)
Header - Asym.Unit
Biol.Unit 1 (25 KB)
Header - Biol.Unit 1
Biol.Unit 2 (23 KB)
Header - Biol.Unit 2
Biol.Unit 3 (90 KB)
Header - Biol.Unit 3
Biol.Unit 4 (46 KB)
Header - Biol.Unit 4
Biol.Unit 5 (46 KB)
Header - Biol.Unit 5
Biol.Unit 6 (46 KB)
Header - Biol.Unit 6
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