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1KVO
Asym. Unit
Info
Asym.Unit (140 KB)
Biol.Unit 1 (47 KB)
Biol.Unit 2 (47 KB)
Biol.Unit 3 (47 KB)
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(1)
Title
:
HUMAN PHOSPHOLIPASE A2 COMPLEXED WITH A HIGHLY POTENT SUBSTRATE ANOLOGUE
Authors
:
S. -S. Cha, S. S. Abdel-Meguid, B. -H. Oh
Date
:
29 Jul 96 (Deposition) - 07 Jul 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Hydrolase, Lipid Degradation, Membrane, Signal, Calcium
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. S. Cha, D. Lee, J. Adams, J. T. Kurdyla, C. S. Jones, L. A. Marshall, B. Bolognese, S. S. Abdel-Meguid, B. H. Oh
High-Resolution X-Ray Crystallography Reveals Precise Binding Interactions Between Human Nonpancreatic Secreted Phospholipase A2 And A Highly Potent Inhibitor (Fpl67047Xx).
J. Med. Chem. V. 39 3878 1996
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 18)
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)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
2a: 4-(S)-[(1-OXO-7-PHENYLHEPTYL)AMINO... (OAPa)
2b: 4-(S)-[(1-OXO-7-PHENYLHEPTYL)AMINO... (OAPb)
2c: 4-(S)-[(1-OXO-7-PHENYLHEPTYL)AMINO... (OAPc)
2d: 4-(S)-[(1-OXO-7-PHENYLHEPTYL)AMINO... (OAPd)
2e: 4-(S)-[(1-OXO-7-PHENYLHEPTYL)AMINO... (OAPe)
2f: 4-(S)-[(1-OXO-7-PHENYLHEPTYL)AMINO... (OAPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
12
Ligand/Ion
CALCIUM ION
2
OAP
6
Ligand/Ion
4-(S)-[(1-OXO-7-PHENYLHEPTYL)AMINO]-5-[4-(PHENYLMETHYL)PHENYLTHIO]PENTANOIC ACID
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:27 , GLY A:29 , GLY A:31 , ASP A:48 , OAP A:190
BINDING SITE FOR RESIDUE CA A 191
02
AC2
SOFTWARE
PHE A:23 , GLY A:25 , TYR A:112 , ASN A:114 , HOH A:1209
BINDING SITE FOR RESIDUE CA A 192
03
AC3
SOFTWARE
HIS B:27 , GLY B:29 , GLY B:31 , ASP B:48 , OAP B:190
BINDING SITE FOR RESIDUE CA B 191
04
AC4
SOFTWARE
PHE B:23 , GLY B:25 , TYR B:112 , ASN B:114 , HOH B:1242
BINDING SITE FOR RESIDUE CA B 192
05
AC5
SOFTWARE
HIS C:27 , GLY C:29 , GLY C:31 , ASP C:48 , OAP C:190
BINDING SITE FOR RESIDUE CA C 191
06
AC6
SOFTWARE
PHE C:23 , TYR C:24 , GLY C:25 , TYR C:112 , ASN C:114 , HOH C:1268
BINDING SITE FOR RESIDUE CA C 192
07
AC7
SOFTWARE
HIS D:27 , GLY D:29 , GLY D:31 , ASP D:48 , OAP D:190
BINDING SITE FOR RESIDUE CA D 191
08
AC8
SOFTWARE
PHE D:23 , GLY D:25 , TYR D:112 , ASN D:114
BINDING SITE FOR RESIDUE CA D 192
09
AC9
SOFTWARE
HIS E:27 , GLY E:29 , GLY E:31 , ASP E:48 , OAP E:190
BINDING SITE FOR RESIDUE CA E 191
10
BC1
SOFTWARE
PHE E:23 , GLY E:25 , TYR E:112 , ASN E:114 , HOH E:1334
BINDING SITE FOR RESIDUE CA E 192
11
BC2
SOFTWARE
HIS F:27 , GLY F:29 , GLY F:31 , ASP F:48 , OAP F:190
BINDING SITE FOR RESIDUE CA F 191
12
BC3
SOFTWARE
PHE F:23 , GLY F:25 , TYR F:112 , ASN F:114 , HOH F:1354 , HOH F:1457
BINDING SITE FOR RESIDUE CA F 192
13
BC4
SOFTWARE
ALA A:17 , ALA A:18 , TYR A:21 , GLY A:22 , HIS A:27 , GLY A:29 , VAL A:30 , GLY A:31 , CYS A:44 , HIS A:47 , ASP A:48 , TYR A:51 , CA A:191
BINDING SITE FOR RESIDUE OAP A 190
14
BC5
SOFTWARE
LEU B:2 , PHE B:5 , ALA B:17 , ALA B:18 , GLY B:22 , HIS B:27 , GLY B:29 , VAL B:30 , GLY B:31 , HIS B:47 , ASP B:48 , TYR B:51 , CA B:191 , HOH B:1462 , HOH B:1486
BINDING SITE FOR RESIDUE OAP B 190
15
BC6
SOFTWARE
LEU C:2 , PHE C:5 , ILE C:9 , ALA C:17 , HIS C:27 , GLY C:29 , VAL C:30 , GLY C:31 , CYS C:44 , HIS C:47 , ASP C:48 , CA C:191
BINDING SITE FOR RESIDUE OAP C 190
16
BC7
SOFTWARE
LEU D:2 , PHE D:5 , GLY D:22 , HIS D:27 , GLY D:29 , VAL D:30 , GLY D:31 , CYS D:44 , HIS D:47 , ASP D:48 , TYR D:51 , CA D:191
BINDING SITE FOR RESIDUE OAP D 190
17
BC8
SOFTWARE
LEU E:2 , PHE E:5 , ALA E:17 , ALA E:18 , GLY E:22 , HIS E:27 , GLY E:29 , VAL E:30 , GLY E:31 , CYS E:44 , HIS E:47 , ASP E:48 , TYR E:51 , CA E:191
BINDING SITE FOR RESIDUE OAP E 190
18
BC9
SOFTWARE
LEU F:2 , PHE F:5 , ILE F:9 , ALA F:17 , TYR F:21 , GLY F:22 , PHE F:23 , HIS F:27 , GLY F:29 , VAL F:30 , GLY F:31 , HIS F:47 , ASP F:48 , TYR F:51 , CA F:191
BINDING SITE FOR RESIDUE OAP F 190
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: PA2_HIS (A:43-50,B:43-50,C:43-50,D:43-50,E:...)
2: PA2_ASP (A:87-97,B:87-97,C:87-97,D:87-97,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PA2_HIS
PS00118
Phospholipase A2 histidine active site.
PA2GA_HUMAN
63-70
6
A:43-50
B:43-50
C:43-50
D:43-50
E:43-50
F:43-50
2
PA2_ASP
PS00119
Phospholipase A2 aspartic acid active site.
PA2GA_HUMAN
107-117
6
A:87-97
B:87-97
C:87-97
D:87-97
E:87-97
F:87-97
[
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]
Exons
(3, 18)
Info
All Exons
Exon 1.3e (A:1-42 | B:1-42 | C:1-42 | D:1-42 ...)
Exon 1.3g (A:42-78 | B:42-78 | C:42-78 | D:42...)
Exon 1.4d (A:78-124 | B:78-124 | C:78-124 | D...)
View:
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All Exon Boundaries
1: Boundary 1.3c/1.3e
2: Boundary 1.3e/1.3g
3: Boundary 1.3g/1.4d
4: Boundary 1.4d/-
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
1.2c
ENST00000400520
2c
ENSE00001543334
chr1:
20306111-20306073
39
PA2GA_HUMAN
-
0
0
-
-
1.3c
ENST00000400520
3c
ENSE00002182826
chr1:
20305372-20305227
146
PA2GA_HUMAN
1-14
14
0
-
-
1.3e
ENST00000400520
3e
ENSE00001326822
chr1:
20305017-20304873
145
PA2GA_HUMAN
14-62
49
6
A:1-42
B:1-42
C:1-42
D:1-42
E:1-42
F:1-42
42
42
42
42
42
42
1.3g
ENST00000400520
3g
ENSE00000873019
chr1:
20304614-20304508
107
PA2GA_HUMAN
62-98
37
6
A:42-78
B:42-78
C:42-78
D:42-78
E:42-78
F:42-78
37
37
37
37
37
37
1.4d
ENST00000400520
4d
ENSE00001543318
chr1:
20302336-20301929
408
PA2GA_HUMAN
98-144
47
6
A:78-124
B:78-124
C:78-124
D:78-124
E:78-124
F:78-124
47
47
47
47
47
47
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1kvoa_ (A:)
1b: SCOP_d1kvoe_ (E:)
1c: SCOP_d1kvof_ (F:)
1d: SCOP_d1kvob_ (B:)
1e: SCOP_d1kvoc_ (C:)
1f: SCOP_d1kvod_ (D:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Phospholipase A2, PLA2
(282)
Superfamily
:
Phospholipase A2, PLA2
(282)
Family
:
Vertebrate phospholipase A2
(271)
Protein domain
:
Phospholipase A2
(72)
Human (Homo sapiens), synovial fluid [TaxId: 9606]
(16)
1a
d1kvoa_
A:
1b
d1kvoe_
E:
1c
d1kvof_
F:
1d
d1kvob_
B:
1e
d1kvoc_
C:
1f
d1kvod_
D:
[
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1kvoA00 (A:1-124)
1b: CATH_1kvoB00 (B:1-124)
1c: CATH_1kvoC00 (C:1-124)
1d: CATH_1kvoD00 (D:1-124)
1e: CATH_1kvoE00 (E:1-124)
1f: CATH_1kvoF00 (F:1-124)
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Phospholipase A2
(241)
Homologous Superfamily
:
Phospholipase A2
(241)
Human (Homo sapiens)
(15)
1a
1kvoA00
A:1-124
1b
1kvoB00
B:1-124
1c
1kvoC00
C:1-124
1d
1kvoD00
D:1-124
1e
1kvoE00
E:1-124
1f
1kvoF00
F:1-124
[
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]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Phospholip_A2_1_1kvoF01 (F:1-120)
1b: PFAM_Phospholip_A2_1_1kvoF02 (F:1-120)
1c: PFAM_Phospholip_A2_1_1kvoF03 (F:1-120)
1d: PFAM_Phospholip_A2_1_1kvoF04 (F:1-120)
1e: PFAM_Phospholip_A2_1_1kvoF05 (F:1-120)
1f: PFAM_Phospholip_A2_1_1kvoF06 (F:1-120)
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)
Clan
:
no clan defined [family: Phospholip_A2_1]
(33)
Family
:
Phospholip_A2_1
(33)
Homo sapiens (Human)
(8)
1a
Phospholip_A2_1-1kvoF01
F:1-120
1b
Phospholip_A2_1-1kvoF02
F:1-120
1c
Phospholip_A2_1-1kvoF03
F:1-120
1d
Phospholip_A2_1-1kvoF04
F:1-120
1e
Phospholip_A2_1-1kvoF05
F:1-120
1f
Phospholip_A2_1-1kvoF06
F:1-120
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