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1M63
Asym. Unit
Info
Asym.Unit (236 KB)
Biol.Unit 1 (226 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CALCINEURIN-CYCLOPHILIN-CYCLOSPORIN SHOWS COMMON BUT DISTINCT RECOGNITION OF IMMUNOPHILIN-DRUG COMPLEXES
Authors
:
Q. Huai, H. -Y. Kim, Y. Liu, Y. Zhao, A. Mondragon, J. O. Liu, H. Ke
Date
:
12 Jul 02 (Deposition) - 25 Sep 02 (Release) - 27 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Hydrolase-Isomerase-Immunosuppressant Complex, Immunophilin, Calcineurin, Cyclosporin A, Immunosuppressant, Cyclophilin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Q. Huai, H. -Y. Kim, Y. Liu, Y. Zhao, A. Mondragon, J. O. Liu, H. Ke
Crystal Structure Of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition Of Immunophilin-Drug Complexes
Proc. Natl. Acad. Sci. Usa V. 99 12037 2002
[
close entry info
]
Hetero Components
(9, 30)
Info
All Hetero Components
1a: ALPHA-AMINOBUTYRIC ACID (ABAa)
1b: ALPHA-AMINOBUTYRIC ACID (ABAb)
2a: 4-METHYL-4-[(E)-2-BUTENYL]-4,N-MET... (BMTa)
2b: 4-METHYL-4-[(E)-2-BUTENYL]-4,N-MET... (BMTb)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
3e: CALCIUM ION (CAe)
3f: CALCIUM ION (CAf)
3g: CALCIUM ION (CAg)
3h: CALCIUM ION (CAh)
4a: D-ALANINE (DALa)
4b: D-ALANINE (DALb)
5a: FE (III) ION (FEa)
5b: FE (III) ION (FEb)
6a: N-METHYLLEUCINE (MLEa)
6b: N-METHYLLEUCINE (MLEb)
6c: N-METHYLLEUCINE (MLEc)
6d: N-METHYLLEUCINE (MLEd)
6e: N-METHYLLEUCINE (MLEe)
6f: N-METHYLLEUCINE (MLEf)
6g: N-METHYLLEUCINE (MLEg)
6h: N-METHYLLEUCINE (MLEh)
7a: N-METHYLVALINE (MVAa)
7b: N-METHYLVALINE (MVAb)
8a: SARCOSINE (SARa)
8b: SARCOSINE (SARb)
9a: ZINC ION (ZNa)
9b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ABA
2
Mod. Amino Acid
ALPHA-AMINOBUTYRIC ACID
2
BMT
2
Mod. Amino Acid
4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
3
CA
8
Ligand/Ion
CALCIUM ION
4
DAL
2
Mod. Amino Acid
D-ALANINE
5
FE
2
Ligand/Ion
FE (III) ION
6
MLE
8
Mod. Amino Acid
N-METHYLLEUCINE
7
MVA
2
Mod. Amino Acid
N-METHYLVALINE
8
SAR
2
Mod. Amino Acid
SARCOSINE
9
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP B:30 , ASP B:32 , SER B:34 , SER B:36 , GLU B:41
BINDING SITE FOR RESIDUE CA B 500
02
AC2
SOFTWARE
ASP B:62 , ASP B:64 , ASN B:66 , GLU B:68 , ASP B:70 , GLU B:73
BINDING SITE FOR RESIDUE CA B 501
03
AC3
SOFTWARE
ASP B:99 , ASP B:101 , ASP B:103 , TYR B:105 , GLU B:110
BINDING SITE FOR RESIDUE CA B 502
04
AC4
SOFTWARE
ASP B:140 , ASP B:142 , ASP B:144 , ARG B:146 , GLU B:151
BINDING SITE FOR RESIDUE CA B 503
05
AC5
SOFTWARE
ASP A:118 , ASN A:150 , HIS A:199 , HIS A:281 , FE A:505
BINDING SITE FOR RESIDUE ZN A 504
06
AC6
SOFTWARE
ASP A:90 , HIS A:92 , ASP A:118 , HIS A:281 , ZN A:504
BINDING SITE FOR RESIDUE FE A 505
07
AC7
SOFTWARE
ASP F:30 , ASP F:32 , SER F:34 , SER F:36 , GLU F:41
BINDING SITE FOR RESIDUE CA F 500
08
AC8
SOFTWARE
ASP F:62 , ASP F:64 , ASN F:66 , GLU F:68 , ASP F:70 , GLU F:73
BINDING SITE FOR RESIDUE CA F 501
09
AC9
SOFTWARE
ASP F:99 , ASP F:101 , ASP F:103 , TYR F:105 , GLU F:110
BINDING SITE FOR RESIDUE CA F 502
10
BC1
SOFTWARE
ASP F:140 , ASP F:142 , ASP F:144 , ARG F:146 , GLU F:151
BINDING SITE FOR RESIDUE CA F 503
11
BC2
SOFTWARE
ASP E:118 , ASN E:150 , HIS E:199 , HIS E:281 , FE E:505
BINDING SITE FOR RESIDUE ZN E 504
12
BC3
SOFTWARE
ASP E:90 , HIS E:92 , ASP E:118 , ZN E:504
BINDING SITE FOR RESIDUE FE E 505
13
BC4
SOFTWARE
SER A:2 , LEU A:312 , TYR A:341 , TRP A:342 , PRO A:344 , TRP A:352 , PHE A:356 , ASN B:122 , ARG C:55 , PHE C:60 , GLN C:63 , GLY C:72 , ALA C:101 , ASN C:102 , GLN C:111 , PHE C:113 , TRP C:121 , LEU C:122 , HIS C:126 , ARG C:148
BINDING SITE FOR CHAIN D OF CYCLOSPORIN A
14
BC5
SOFTWARE
LEU E:312 , VAL E:314 , TYR E:341 , TRP E:342 , PRO E:344 , TRP E:352 , PHE E:356 , ASN F:122 , LEU F:123 , ARG G:55 , PHE G:60 , GLN G:63 , GLY G:72 , ALA G:101 , ASN G:102 , ALA G:103 , GLN G:111 , PHE G:113 , TRP G:121 , LEU G:122 , HIS G:126
BINDING SITE FOR CHAIN H OF CYCLOSPORIN A
[
close Site info
]
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
(5, 22)
Info
All PROSITE Patterns/Profiles
1: CSA_PPIASE_2 (C:7-163,G:7-163)
2: EF_HAND_1 (B:30-42,F:30-42|B:62-74,F:62-74|B:...)
3: CSA_PPIASE_1 (C:48-65,G:48-65)
4: EF_HAND_2 (B:49-84,F:49-84|B:17-45,F:17-45|B:...)
5: SER_THR_PHOSPHATASE (A:147-152,E:147-152)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CSA_PPIASE_2
PS50072
Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.
PPIA_HUMAN
7-163
2
C:7-163
G:7-163
2
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
CANB1_HUMAN
31-43
63-75
100-112
141-153
8
B:30-42
F:30-42
B:62-74
F:62-74
B:99-111
F:99-111
B:140-152
F:140-152
3
CSA_PPIASE_1
PS00170
Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.
PPIA_HUMAN
48-65
2
C:48-65
G:48-65
4
EF_HAND_2
PS50222
EF-hand calcium-binding domain profile.
CANB1_HUMAN
50-85
18-46
87-122
128-163
8
B:49-84
F:49-84
B:17-45
F:17-45
B:86-121
F:86-121
B:127-162
F:127-162
5
SER_THR_PHOSPHATASE
PS00125
Serine/threonine specific protein phosphatases signature.
PP2BA_HUMAN
147-152
2
A:147-152
E:147-152
[
close PROSITE info
]
Exons
(15, 30)
Info
All Exons
Exon 1.6 (B:12-14 | F:10-14)
Exon 1.7 (B:14-73 | F:14-73)
Exon 1.8 (B:73-93 | F:73-93)
Exon 1.9 (B:93-154 | F:93-154)
Exon 1.10c (B:155-169 | F:155-169)
Exon 2.2b (A:1-20 | E:14-20)
Exon 2.3a (A:20-87 | E:20-87)
Exon 2.6 (A:87-128 | E:87-128)
Exon 2.8 (A:129-166 | E:129-166)
Exon 2.9c (A:166-214 | E:166-214)
Exon 2.10b (A:215-261 | E:215-261)
Exon 2.11b (A:261-287 | E:261-287)
Exon 2.12 (A:287-319 | E:287-319)
Exon 2.13 (A:319-361 | E:319-361)
Exon 2.14 (A:361-372 | E:361-372)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.4/1.6
02: Boundary 1.6/1.7
03: Boundary 1.7/1.8
04: Boundary 1.8/1.9
05: Boundary 1.9/1.10c
06: Boundary 1.10c/-
07: Boundary -/2.2b
08: Boundary 2.2b/2.3a
09: Boundary 2.3a/2.6
10: Boundary 2.6/2.8
11: Boundary 2.8/2.9c
12: Boundary 2.9c/2.10b
13: Boundary 2.10b/2.11b
14: Boundary 2.11b/2.12
15: Boundary 2.12/2.13
16: Boundary 2.13/2.14
17: Boundary 2.14/2.15
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
1.4
ENST00000234310
4
ENSE00001191356
chr2:
68479663-68479257
407
CANB1_HUMAN
1-1
1
0
-
-
1.6
ENST00000234310
6
ENSE00001806348
chr2:
68444263-68444224
40
CANB1_HUMAN
2-15
14
2
B:12-14
F:10-14
3
5
1.7
ENST00000234310
7
ENSE00001434958
chr2:
68415822-68415646
177
CANB1_HUMAN
15-74
60
2
B:14-73
F:14-73
60
60
1.8
ENST00000234310
8
ENSE00000758788
chr2:
68414446-68414387
60
CANB1_HUMAN
74-94
21
2
B:73-93
F:73-93
21
21
1.9
ENST00000234310
9
ENSE00000810241
chr2:
68413784-68413600
185
CANB1_HUMAN
94-155
62
2
B:93-154
F:93-154
62
62
1.10c
ENST00000234310
10c
ENSE00001191364
chr2:
68408142-68405989
2154
CANB1_HUMAN
156-170
15
2
B:155-169
F:155-169
15
15
2.2b
ENST00000394854
2b
ENSE00001896251
chr4:
102268637-102267896
742
PP2BA_HUMAN
1-20
20
2
A:1-20
E:14-20
20
7
2.3a
ENST00000394854
3a
ENSE00000934976
chr4:
102117273-102117073
201
PP2BA_HUMAN
20-87
68
2
A:20-87
E:20-87
68
68
2.6
ENST00000394854
6
ENSE00000970132
chr4:
102030235-102030111
125
PP2BA_HUMAN
87-128
42
2
A:87-128
E:87-128
42
42
2.8
ENST00000394854
8
ENSE00001628359
chr4:
102020879-102020768
112
PP2BA_HUMAN
129-166
38
2
A:129-166
E:129-166
38
38
2.9c
ENST00000394854
9c
ENSE00000970134
chr4:
102019669-102019524
146
PP2BA_HUMAN
166-214
49
2
A:166-214
E:166-214
49
49
2.10b
ENST00000394854
10b
ENSE00001080696
chr4:
102015072-102014933
140
PP2BA_HUMAN
215-261
47
2
A:215-261
E:215-261
47
47
2.11b
ENST00000394854
11b
ENSE00001720711
chr4:
102004420-102004343
78
PP2BA_HUMAN
261-287
27
2
A:261-287
E:261-287
27
27
2.12
ENST00000394854
12
ENSE00000970136
chr4:
102001783-102001689
95
PP2BA_HUMAN
287-319
33
2
A:287-319
E:287-319
33
33
2.13
ENST00000394854
13
ENSE00001781830
chr4:
101984514-101984389
126
PP2BA_HUMAN
319-361
43
2
A:319-361
E:319-361
43
43
2.14
ENST00000394854
14
ENSE00001080697
chr4:
101982318-101982244
75
PP2BA_HUMAN
361-386
26
2
A:361-372
E:361-372
12
12
2.15
ENST00000394854
15
ENSE00001080695
chr4:
101961723-101961639
85
PP2BA_HUMAN
386-414
29
0
-
-
2.16
ENST00000394854
16
ENSE00000934972
chr4:
101953521-101953424
98
PP2BA_HUMAN
414-447
34
0
-
-
2.17
ENST00000394854
17
ENSE00001797567
chr4:
101950352-101950323
30
PP2BA_HUMAN
447-457
11
0
-
-
2.18e
ENST00000394854
18e
ENSE00001284009
chr4:
101947218-101944587
2632
PP2BA_HUMAN
457-521
65
0
-
-
[
close EXON info
]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1m63b_ (B:)
1b: SCOP_d1m63f_ (F:)
2a: SCOP_d1m63c_ (C:)
2b: SCOP_d1m63g_ (G:)
3a: SCOP_d1m63a_ (A:)
3b: SCOP_d1m63e_ (E:)
View:
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Folds
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Superfamilies
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)
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)
Families
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
EF Hand-like
(739)
Superfamily
:
EF-hand
(657)
Family
:
Calmodulin-like
(356)
Protein domain
:
Calcineurin regulatory subunit (B-chain)
(6)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d1m63b_
B:
1b
d1m63f_
F:
Class
:
All beta proteins
(24004)
Fold
:
Cyclophilin-like
(169)
Superfamily
:
Cyclophilin-like
(169)
Family
:
Cyclophilin (peptidylprolyl isomerase)
(160)
Protein domain
:
Cyclophilin (eukaryotic)
(77)
Human (Homo sapiens), variant A [TaxId: 9606]
(58)
2a
d1m63c_
C:
2b
d1m63g_
G:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Metallo-dependent phosphatases
(115)
Superfamily
:
Metallo-dependent phosphatases
(115)
Family
:
Protein serine/threonine phosphatase
(50)
Protein domain
:
Protein phosphatase-2B (PP-2B, calcineurin A subunit)
(6)
Human (Homo sapiens) [TaxId: 9606]
(5)
3a
d1m63a_
A:
3b
d1m63e_
E:
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1m63E00 (E:14-372)
1b: CATH_1m63A00 (A:1-372)
2a: CATH_1m63B00 (B:12-169)
2b: CATH_1m63F00 (F:10-169)
3a: CATH_1m63C00 (C:1-165)
3b: CATH_1m63G00 (G:1-165)
View:
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Architectures
(
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(
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Purple Acid Phosphatase; chain A, domain 2
(87)
Homologous Superfamily
:
[code=3.60.21.10, no name defined]
(83)
Human (Homo sapiens)
(36)
1a
1m63E00
E:14-372
1b
1m63A00
A:1-372
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Recoverin; domain 1
(474)
Homologous Superfamily
:
EF-hand
(412)
Human (Homo sapiens)
(106)
2a
1m63B00
B:12-169
2b
1m63F00
F:10-169
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Cyclophilin
(95)
Homologous Superfamily
:
Cyclophilin
(95)
Human (Homo sapiens)
(58)
3a
1m63C00
C:1-165
3b
1m63G00
G:1-165
[
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]
Pfam Domains
(5, 12)
Info
all PFAM domains
1a: PFAM_Metallophos_1m63E01 (E:83-285)
1b: PFAM_Metallophos_1m63E02 (E:83-285)
2a: PFAM_Pro_isomerase_1m63G01 (G:7-163)
2b: PFAM_Pro_isomerase_1m63G02 (G:7-163)
3a: PFAM_EF_hand_3_1m63F01 (F:22-46)
3b: PFAM_EF_hand_3_1m63F02 (F:22-46)
4a: PFAM_EF_hand_5_1m63F03 (F:90-156)
4b: PFAM_EF_hand_5_1m63F04 (F:90-156)
4c: PFAM_EF_hand_5_1m63F05 (F:90-156)
4d: PFAM_EF_hand_5_1m63F06 (F:90-156)
5a: PFAM_efhand_1m63F07 (F:90-118)
5b: PFAM_efhand_1m63F08 (F:90-118)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Calcineurin
(56)
Family
:
Metallophos
(45)
Homo sapiens (Human)
(15)
1a
Metallophos-1m63E01
E:83-285
1b
Metallophos-1m63E02
E:83-285
Clan
:
Cyclophil-like
(65)
Family
:
Pro_isomerase
(53)
Homo sapiens (Human)
(42)
2a
Pro_isomerase-1m63G01
G:7-163
2b
Pro_isomerase-1m63G02
G:7-163
Clan
:
EF_hand
(270)
Family
:
EF_hand_3
(27)
Homo sapiens (Human)
(6)
3a
EF_hand_3-1m63F01
F:22-46
3b
EF_hand_3-1m63F02
F:22-46
Family
:
EF_hand_5
(126)
Homo sapiens (Human)
(31)
4a
EF_hand_5-1m63F03
F:90-156
4b
EF_hand_5-1m63F04
F:90-156
4c
EF_hand_5-1m63F05
F:90-156
4d
EF_hand_5-1m63F06
F:90-156
Family
:
efhand
(70)
Homo sapiens (Human)
(8)
5a
efhand-1m63F07
F:90-118
5b
efhand-1m63F08
F:90-118
[
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]
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Chain C
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Chain H
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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