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1SU3
Biol. Unit 3
Info
Asym.Unit (155 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (75 KB)
Biol.Unit 3 (563 KB)
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(1)
Title
:
X-RAY STRUCTURE OF HUMAN PROMMP-1: NEW INSIGHTS INTO COLLAGENASE ACTION
Authors
:
D. Jozic, G. Bourenkov, N. H. Lim, H. Nagase, W. Bode, K. Maskos, Structural Proteomics In Europe (Spine)
Date
:
26 Mar 04 (Deposition) - 21 Dec 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: B (8x)
Keywords
:
Prodomain, Hemopexin Domain, Exocite, Structural Proteomics In Europe, Spine, Structural Genomics, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Jozic, G. Bourenkov, N. H. Lim, R. Visse, H. Nagase, W. Bode, K. Maskos
X-Ray Structure Of Human Prommp-1: New Insights Into Procollagenase Activation And Collagen Binding.
J. Biol. Chem. V. 280 9578 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 40)
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)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
EPE
8
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
NA
-1
Ligand/Ion
SODIUM ION
5
SO4
32
Ligand/Ion
SULFATE ION
6
ZN
-1
Ligand/Ion
ZINC ION
[
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]
Sites
(13, 13)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC6 (SOFTWARE)
08: BC7 (SOFTWARE)
09: BC8 (SOFTWARE)
10: BC9 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
ALA B:157 , ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194
BINDING SITE FOR RESIDUE CA B 905
02
AC6
SOFTWARE
ASP B:175 , GLY B:176 , GLY B:178 , ASN B:180 , ASP B:198 , GLU B:201
BINDING SITE FOR RESIDUE CA B 906
03
AC7
SOFTWARE
ASP B:124 , GLU B:199 , GLU B:201 , HOH B:1085
BINDING SITE FOR RESIDUE CA B 907
04
AC8
SOFTWARE
ASP B:285 , GLU B:329 , ASP B:378 , ASP B:427 , HOH B:1052 , HOH B:1053 , HOH B:1080
BINDING SITE FOR RESIDUE CA B 908
05
BC1
SOFTWARE
ILE B:287 , ALA B:331 , ALA B:380 , ALA B:428 , VAL B:429 , NA B:912
BINDING SITE FOR RESIDUE CL B 910
06
BC3
SOFTWARE
ILE B:287 , ALA B:331 , ALA B:380 , VAL B:429 , CL B:910 , HOH B:980
BINDING SITE FOR RESIDUE NA B 912
07
BC6
SOFTWARE
CYS B:92 , HIS B:218 , HIS B:222 , HIS B:228
BINDING SITE FOR RESIDUE ZN B 913
08
BC7
SOFTWARE
HIS B:168 , ASP B:170 , HIS B:183 , HIS B:196
BINDING SITE FOR RESIDUE ZN B 915
09
BC8
SOFTWARE
PRO B:189 , GLY B:190 , LYS B:404
BINDING SITE FOR RESIDUE SO4 B 500
10
BC9
SOFTWARE
ASP B:167 , HIS B:168 , ARG B:169 , ASP B:170 , ASN B:171 , PRO B:173 , HOH B:946
BINDING SITE FOR RESIDUE SO4 B 501
11
CC1
SOFTWARE
PRO B:126 , ARG B:127
BINDING SITE FOR RESIDUE SO4 B 504
12
CC2
SOFTWARE
SER B:142 , THR B:145 , SER B:263 , GLN B:264 , ASN B:265 , HOH B:918
BINDING SITE FOR RESIDUE SO4 B 503
13
CC4
SOFTWARE
VAL B:94 , PRO B:95 , SER B:172 , ALA B:184 , PHE B:185 , GLN B:186 , HOH B:959
BINDING SITE FOR RESIDUE EPE B 600
[
close Site info
]
SAPs(SNPs)/Variants
(5, 40)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_021024 (I191V, chain B, )
2: VAR_011970 (D252G, chain B, )
3: VAR_054005 (R262S, chain B, )
4: VAR_021025 (R405Q, chain B, )
5: VAR_021026 (S406T, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021024
I
191
V
MMP1_HUMAN
Polymorphism
17879973
B
I
191
V
2
UniProt
VAR_011970
D
252
G
MMP1_HUMAN
Polymorphism
513964
B
D
252
G
3
UniProt
VAR_054005
R
262
S
MMP1_HUMAN
Polymorphism
12282811
B
R
262
S
4
UniProt
VAR_021025
R
405
Q
MMP1_HUMAN
Polymorphism
17879165
B
R
405
Q
5
UniProt
VAR_021026
S
406
T
MMP1_HUMAN
Polymorphism
17884120
B
S
406
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 56)
Info
All PROSITE Patterns/Profiles
1: CYSTEINE_SWITCH (B:90-97)
2: ZINC_PROTEASE (B:215-224)
3: HEMOPEXIN_2 (B:423-465)
4: HEMOPEXIN (B:317-332)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYSTEINE_SWITCH
PS00546
Matrixins cysteine switch.
MMP1_HUMAN
90-97
8
-
B:90-97
2
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
MMP1_HUMAN
215-224
8
-
B:215-224
3
HEMOPEXIN_2
PS51642
Hemopexin repeat profile.
MMP1_HUMAN
275-324
325-371
374-422
423-466
32
-
B:275-324
-
B:325-371
-
B:374-422
-
B:423-465
4
HEMOPEXIN
PS00024
Hemopexin domain signature.
MMP1_HUMAN
317-332
8
-
B:317-332
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1su3a1 (A:32-98)
1b: SCOP_d1su3b1 (B:32-98)
2a: SCOP_d1su3a2 (A:271-465)
2b: SCOP_d1su3b2 (B:271-465)
3a: SCOP_d1su3a3 (A:107-270)
3b: SCOP_d1su3b3 (B:107-270)
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(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
PGBD-like
(9)
Superfamily
:
PGBD-like
(9)
Family
:
MMP N-terminal domain
(6)
Protein domain
:
Fibroblast collagenase (MMP-1)
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1su3a1
A:32-98
1b
d1su3b1
B:32-98
Class
:
All beta proteins
(24004)
Fold
:
4-bladed beta-propeller
(15)
Superfamily
:
Hemopexin-like domain
(15)
Family
:
Hemopexin-like domain
(12)
Protein domain
:
Collagenase (MMP1), C-terminal domain
(2)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1su3a2
A:271-465
2b
d1su3b2
B:271-465
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
Metalloproteases (zincins), catalytic domain
(647)
Family
:
Matrix metalloproteases, catalytic domain
(199)
Protein domain
:
Fibroblast collagenase (MMP-1)
(14)
Human (Homo sapiens) [TaxId: 9606]
(13)
3a
d1su3a3
A:107-270
3b
d1su3b3
B:107-270
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1su3A01 (A:32-269)
1b: CATH_1su3B01 (B:31-269)
2a: CATH_1su3A02 (A:270-466)
2b: CATH_1su3B02 (B:270-465)
View:
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Classes
(
)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Collagenase (Catalytic Domain)
(236)
Homologous Superfamily
:
Collagenase (Catalytic Domain)
(234)
Human (Homo sapiens)
(153)
1a
1su3A01
A:32-269
1b
1su3B01
B:31-269
Class
:
Mainly Beta
(13760)
Architecture
:
4 Propellor
(14)
Topology
:
Hemopexin
(14)
Homologous Superfamily
:
Hemopexin
(14)
Human (Homo sapiens)
(10)
2a
1su3A02
A:270-466
2b
1su3B02
B:270-465
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_PG_binding_1_1su3B01 (B:31-87)
1b: PFAM_PG_binding_1_1su3B02 (B:31-87)
2a: PFAM_Peptidase_M10_1su3B03 (B:108-261)
2b: PFAM_Peptidase_M10_1su3B04 (B:108-261)
3a: PFAM_Hemopexin_1su3B05 (B:426-465)
3b: PFAM_Hemopexin_1su3B06 (B:426-465)
3c: PFAM_Hemopexin_1su3B07 (B:426-465)
3d: PFAM_Hemopexin_1su3B08 (B:426-465)
3e: PFAM_Hemopexin_1su3B09 (B:426-465)
3f: PFAM_Hemopexin_1su3B10 (B:426-465)
3g: PFAM_Hemopexin_1su3B11 (B:426-465)
3h: PFAM_Hemopexin_1su3B12 (B:426-465)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PGBD
(5)
Family
:
PG_binding_1
(4)
Homo sapiens (Human)
(3)
1a
PG_binding_1-1su3B01
B:31-87
1b
PG_binding_1-1su3B02
B:31-87
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
2a
Peptidase_M10-1su3B03
B:108-261
2b
Peptidase_M10-1su3B04
B:108-261
Clan
:
no clan defined [family: Hemopexin]
(5)
Family
:
Hemopexin
(5)
Homo sapiens (Human)
(3)
3a
Hemopexin-1su3B05
B:426-465
3b
Hemopexin-1su3B06
B:426-465
3c
Hemopexin-1su3B07
B:426-465
3d
Hemopexin-1su3B08
B:426-465
3e
Hemopexin-1su3B09
B:426-465
3f
Hemopexin-1su3B10
B:426-465
3g
Hemopexin-1su3B11
B:426-465
3h
Hemopexin-1su3B12
B:426-465
[
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