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1NB3
Asym. Unit
Info
Asym.Unit (228 KB)
Biol.Unit 1 (58 KB)
Biol.Unit 2 (58 KB)
Biol.Unit 3 (59 KB)
Biol.Unit 4 (58 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF STEFIN A IN COMPLEX WITH CATHEPSIN H: N-TERMINAL RESIDUES OF INHIBITORS CAN ADAPT TO THE ACTIVE SITES OF ENDO-AND EXOPEPTIDASES
Authors
:
S. Jenko, I. Dolenc, G. Guncar, A. Dobersek, M. Podobnik, D. Turk
Date
:
02 Dec 02 (Deposition) - 18 Feb 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,I,J,K,L,P,R,S,T
Biol. Unit 1: A,I,P (1x)
Biol. Unit 2: B,J,R (1x)
Biol. Unit 3: C,K,S (1x)
Biol. Unit 4: D,L,T (1x)
Keywords
:
Cysteine Proteinase, Aminopeptidase, Cystatin, Enzyme-Inhibitor Complex, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Jenko, I. Dolenc, G. Guncar, A. Dobersek, M. Podobnik, D. Turk
Crystal Structure Of Stefin A In Complex With Cathepsin H: N-Terminal Residues Of Inhibitors Can Adapt To The Active Sites Of Endo- And Exopeptidases
J. Mol. Biol. V. 326 875 2003
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
4
Ligand/Ion
BETA-D-MANNOSE
2
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:69 , GLU A:73 , ASN A:112 , NAG A:214 , GLU P:76 , PRO P:77 , GLN P:78
BINDING SITE FOR RESIDUE NAG A 213
02
AC2
SOFTWARE
PHE A:58B , GLN A:70 , GLU A:73 , NAG A:213 , BMA A:215
BINDING SITE FOR RESIDUE NAG A 214
03
AC3
SOFTWARE
TYR A:77 , NAG A:214 , HOH A:252
BINDING SITE FOR RESIDUE BMA A 215
04
AC4
SOFTWARE
SER B:69 , GLN B:70 , GLU B:73 , ASN B:112 , NAG B:214 , GLU R:76 , PRO R:77 , GLN R:78
BINDING SITE FOR RESIDUE NAG B 213
05
AC5
SOFTWARE
PHE B:58B , GLN B:70 , GLU B:73 , TYR B:77 , NAG B:213 , BMA B:215
BINDING SITE FOR RESIDUE NAG B 214
06
AC6
SOFTWARE
PHE B:58B , TYR B:77 , NAG B:214 , HOH B:310 , HOH B:324
BINDING SITE FOR RESIDUE BMA B 215
07
AC7
SOFTWARE
GLU C:73 , ASN C:112 , NAG C:214 , GLU S:76 , PRO S:77 , GLN S:78
BINDING SITE FOR RESIDUE NAG C 213
08
AC8
SOFTWARE
PHE C:58B , GLN C:70 , GLU C:73 , TYR C:77 , NAG C:213 , BMA C:215
BINDING SITE FOR RESIDUE NAG C 214
09
AC9
SOFTWARE
PHE C:58B , TYR C:77 , NAG C:214 , HOH C:252 , HOH C:266
BINDING SITE FOR RESIDUE BMA C 215
10
BC1
SOFTWARE
GLU D:73 , ASN D:112 , NAG D:214 , GLU T:76 , PRO T:77 , GLN T:78
BINDING SITE FOR RESIDUE NAG D 213
11
BC2
SOFTWARE
PHE D:58B , GLN D:70 , GLU D:73 , TYR D:77 , NAG D:213 , BMA D:215
BINDING SITE FOR RESIDUE NAG D 214
12
BC3
SOFTWARE
TYR D:77 , NAG D:214 , HOH D:293 , HOH D:298
BINDING SITE FOR RESIDUE BMA D 215
[
close Site info
]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_048851 (T123M, chain I/J/K/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_048851
T
96
M
CYTA_HUMAN
Polymorphism
34173813
I/J/K/L
T
123
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(4, 16)
Info
All PROSITE Patterns/Profiles
1: CYSTATIN (I:52-65,J:52-65,K:52-65,L:52-65)
2: THIOL_PROTEASE_CYS (A:19-30,B:19-30,C:19-30,D:19-30)
3: THIOL_PROTEASE_HIS (A:157-167,B:157-167,C:157-167,D:15...)
4: THIOL_PROTEASE_ASN (A:170-189,B:170-189,C:170-189,D:17...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYSTATIN
PS00287
Cysteine proteases inhibitors signature.
CYTA_HUMAN
45-58
4
I:52-65
J:52-65
K:52-65
L:52-65
2
THIOL_PROTEASE_CYS
PS00139
Eukaryotic thiol (cysteine) proteases cysteine active site.
CATH_PIG
135-146
4
A:19-30
B:19-30
C:19-30
D:19-30
3
THIOL_PROTEASE_HIS
PS00639
Eukaryotic thiol (cysteine) proteases histidine active site.
CATH_PIG
279-289
4
A:157-167
B:157-167
C:157-167
D:157-167
4
THIOL_PROTEASE_ASN
PS00640
Eukaryotic thiol (cysteine) proteases asparagine active site.
CATH_PIG
296-315
4
A:170-189
B:170-189
C:170-189
D:170-189
[
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]
Exons
(3, 12)
Info
All Exons
Exon 1.1a (I:6-27 | J:6-27 | K:6-27 | L:6-27)
Exon 1.2a (I:28-63 (gaps) | J:28-63 (gaps) | ...)
Exon 1.3 (I:64-125 (gaps) | J:64-125 (gaps) ...)
View:
Select:
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All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2a
3: Boundary 1.2a/1.3
4: Boundary 1.3/-
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
1.1a
ENST00000264474
1a
ENSE00001154693
chr3:
122044091-122044205
115
CYTA_HUMAN
1-22
22
4
I:6-27
J:6-27
K:6-27
L:6-27
22
22
22
22
1.2a
ENST00000264474
2a
ENSE00001078746
chr3:
122056394-122056495
102
CYTA_HUMAN
23-56
34
4
I:28-63 (gaps)
J:28-63 (gaps)
K:28-63 (gaps)
L:28-63 (gaps)
36
36
36
36
1.3
ENST00000264474
3
ENSE00001154683
chr3:
122060286-122060819
534
CYTA_HUMAN
57-98
42
4
I:64-125 (gaps)
J:64-125 (gaps)
K:64-125 (gaps)
L:64-125 (gaps)
65
65
65
65
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1nb3i_ (I:)
1b: SCOP_d1nb3j_ (J:)
1c: SCOP_d1nb3k_ (K:)
1d: SCOP_d1nb3l_ (L:)
2a: SCOP_d1nb3_1 (P:,A:)
2b: SCOP_d1nb3_2 (R:,B:)
2c: SCOP_d1nb3_3 (S:,C:)
2d: SCOP_d1nb3_4 (T:,D:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
Cystatin/monellin
(68)
Family
:
Cystatins
(31)
Protein domain
:
Cystatin A (stefin A)
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d1nb3i_
I:
1b
d1nb3j_
J:
1c
d1nb3k_
K:
1d
d1nb3l_
L:
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
Papain-like
(200)
Protein domain
:
Cathepsin H
(3)
Pig (Sus scrofa) [TaxId: 9823]
(3)
2a
d1nb3.1
P:,A:
2b
d1nb3.2
R:,B:
2c
d1nb3.3
S:,C:
2d
d1nb3.4
T:,D:
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1nb3A00 (A:1-212A)
1b: CATH_1nb3B00 (B:1-212A)
1c: CATH_1nb3C00 (C:1-212A)
1d: CATH_1nb3D00 (D:1-212A)
2a: CATH_1nb3I00 (I:6-125)
2b: CATH_1nb3J00 (J:6-125)
2c: CATH_1nb3K00 (K:6-125)
2d: CATH_1nb3L00 (L:6-125)
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Cathepsin B; Chain A
(207)
Homologous Superfamily
:
Cysteine proteinases
(207)
Pig (Sus scrofa)
(3)
1a
1nb3A00
A:1-212A
1b
1nb3B00
B:1-212A
1c
1nb3C00
C:1-212A
1d
1nb3D00
D:1-212A
Architecture
:
Roll
(3276)
Topology
:
Nuclear Transport Factor 2; Chain: A,
(517)
Homologous Superfamily
:
[code=3.10.450.10, no name defined]
(37)
Pig (Sus scrofa)
(7)
2a
1nb3I00
I:6-125
2b
1nb3J00
J:6-125
2c
1nb3K00
K:6-125
2d
1nb3L00
L:6-125
[
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]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Cystatin_1nb3L01 (L:9-119)
1b: PFAM_Cystatin_1nb3L02 (L:9-119)
1c: PFAM_Cystatin_1nb3L03 (L:9-119)
1d: PFAM_Cystatin_1nb3L04 (L:9-119)
2a: PFAM_Peptidase_C1_1nb3D01 (D:1-210)
2b: PFAM_Peptidase_C1_1nb3D02 (D:1-210)
2c: PFAM_Peptidase_C1_1nb3D03 (D:1-210)
2d: PFAM_Peptidase_C1_1nb3D04 (D:1-210)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cystatin
(20)
Family
:
Cystatin
(15)
Homo sapiens (Human)
(12)
1a
Cystatin-1nb3L01
L:9-119
1b
Cystatin-1nb3L02
L:9-119
1c
Cystatin-1nb3L03
L:9-119
1d
Cystatin-1nb3L04
L:9-119
Clan
:
Peptidase_CA
(169)
Family
:
Peptidase_C1
(81)
Sus scrofa (Pig)
(2)
2a
Peptidase_C1-1nb3D01
D:1-210
2b
Peptidase_C1-1nb3D02
D:1-210
2c
Peptidase_C1-1nb3D03
D:1-210
2d
Peptidase_C1-1nb3D04
D:1-210
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Asym.Unit (228 KB)
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