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1QIC
Asym. Unit
Info
Asym.Unit (111 KB)
Biol.Unit 1 (29 KB)
Biol.Unit 2 (29 KB)
Biol.Unit 3 (29 KB)
Biol.Unit 4 (29 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF STROMELYSIN CATALYTIC DOMAIN
Authors
:
M. G. Williams, Q. -Z. Ye, F. Molina, L. L. Johnson, D. F. Ortwine, A. G. Pavlovsky, J. R. Rubin, R. W. Skeean, A. D. White, T. L. Blundell, C. Humblet, D. J. Hupe, V. Dhanaraj
Date
:
11 Jun 99 (Deposition) - 11 Feb 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Inhibitor, Matrixin, Matrix Metalloproteinase-3 (Mmp-3), Stromelysin-1, Metzincin, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. G. Pavlovsky, M. G. Williams, Q. -Z. Ye, D. F. Ortwine, C. F. Purchase 2Nd, A. D. White, V. Dhanaraj, B. D. Roth, L. L. Johnson, D. J. Hupe, C. Humblet, T. L. Blundell
X-Ray Structure Of Human Stromelysin Catalytic Domain Complexed With Nonpeptide Inhibitors: Implications For Inhibitor Selectivity
Protein Sci. V. 8 1455 1999
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 20)
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: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
12
Ligand/Ion
CALCIUM ION
2
ZN
8
Ligand/Ion
ZINC ION
[
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Sites
(20, 20)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:201 , HIS A:205 , HIS A:211
BINDING SITE FOR RESIDUE ZN A 501
02
AC2
SOFTWARE
HIS A:151 , ASP A:153 , HIS A:166 , HIS A:179
BINDING SITE FOR RESIDUE ZN A 502
03
AC3
SOFTWARE
HIS B:201 , HIS B:205 , HIS B:211
BINDING SITE FOR RESIDUE ZN B 501
04
AC4
SOFTWARE
HIS B:151 , ASP B:153 , HIS B:166 , HIS B:179
BINDING SITE FOR RESIDUE ZN B 502
05
AC5
SOFTWARE
HIS C:201 , HIS C:205 , HIS C:211
BINDING SITE FOR RESIDUE ZN C 501
06
AC6
SOFTWARE
HIS C:151 , ASP C:153 , HIS C:166 , HIS C:179
BINDING SITE FOR RESIDUE ZN C 502
07
AC7
SOFTWARE
HIS D:201 , HIS D:205 , HIS D:211
BINDING SITE FOR RESIDUE ZN D 501
08
AC8
SOFTWARE
HIS D:151 , ASP D:153 , HIS D:166 , HIS D:179
BINDING SITE FOR RESIDUE ZN D 502
09
AC9
SOFTWARE
ASP A:158 , GLY A:159 , GLY A:161 , VAL A:163 , ASP A:181 , GLU A:184
BINDING SITE FOR RESIDUE CA A 503
10
BC1
SOFTWARE
ALA A:140 , ASP A:141 , GLY A:173 , ASN A:175 , ASP A:177 , HOH A:301
BINDING SITE FOR RESIDUE CA A 504
11
BC2
SOFTWARE
ASP A:107 , ASP A:182 , GLU A:184 , HOH A:302
BINDING SITE FOR RESIDUE CA A 505
12
BC3
SOFTWARE
ASP B:158 , GLY B:159 , GLY B:161 , VAL B:163 , ASP B:181 , GLU B:184
BINDING SITE FOR RESIDUE CA B 503
13
BC4
SOFTWARE
ALA B:140 , ASP B:141 , GLY B:173 , ASN B:175 , ASP B:177 , HOH B:303
BINDING SITE FOR RESIDUE CA B 504
14
BC5
SOFTWARE
ASP B:107 , ASP B:182 , GLU B:184
BINDING SITE FOR RESIDUE CA B 505
15
BC6
SOFTWARE
ASP C:158 , GLY C:159 , GLY C:161 , VAL C:163 , ASP C:181 , GLU C:184
BINDING SITE FOR RESIDUE CA C 503
16
BC7
SOFTWARE
ALA C:140 , ASP C:141 , GLY C:173 , ASN C:175 , ASP C:177 , HOH C:305
BINDING SITE FOR RESIDUE CA C 504
17
BC8
SOFTWARE
ASP C:107 , ASP C:182 , GLU C:184 , HOH C:306
BINDING SITE FOR RESIDUE CA C 505
18
BC9
SOFTWARE
ASP D:158 , GLY D:159 , GLY D:161 , VAL D:163 , ASP D:181 , GLU D:184
BINDING SITE FOR RESIDUE CA D 503
19
CC1
SOFTWARE
ALA D:140 , ASP D:141 , GLY D:173 , ASN D:175 , ASP D:177 , HOH D:307
BINDING SITE FOR RESIDUE CA D 504
20
CC2
SOFTWARE
ASP D:107 , ASP D:182 , GLU D:184 , HOH D:308
BINDING SITE FOR RESIDUE CA D 505
[
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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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:198-207,B:198-207,C:198-207,D:19...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
MMP3_HUMAN
215-224
4
A:198-207
B:198-207
C:198-207
D:198-207
[
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]
Exons
(5, 20)
Info
All Exons
Exon 1.2 (A:89-100 | B:89-100 | C:89-100 | D...)
Exon 1.3 (A:100-150 | B:100-150 | C:100-150 ...)
Exon 1.4b (A:150-192 | B:150-192 | C:150-192 ...)
Exon 1.5 (A:192-247 | B:192-247 | C:192-247 ...)
Exon 1.6 (A:247-249 | B:247-249 | C:247-249 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4b
4: Boundary 1.4b/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
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
ENST00000299855
1a
ENSE00002171374
chr11:
102714534-102714173
362
MMP3_HUMAN
1-35
35
0
-
-
1.2
ENST00000299855
2
ENSE00001105428
chr11:
102713647-102713403
245
MMP3_HUMAN
36-117
82
4
A:89-100
B:89-100
C:89-100
D:89-100
12
12
12
12
1.3
ENST00000299855
3
ENSE00001642002
chr11:
102713310-102713162
149
MMP3_HUMAN
117-167
51
4
A:100-150
B:100-150
C:100-150
D:100-150
51
51
51
51
1.4b
ENST00000299855
4b
ENSE00001105420
chr11:
102713010-102712885
126
MMP3_HUMAN
167-209
43
4
A:150-192
B:150-192
C:150-192
D:150-192
43
43
43
43
1.5
ENST00000299855
5
ENSE00001657829
chr11:
102711324-102711160
165
MMP3_HUMAN
209-264
56
4
A:192-247
B:192-247
C:192-247
D:192-247
56
56
56
56
1.6
ENST00000299855
6
ENSE00001105427
chr11:
102710983-102710839
145
MMP3_HUMAN
264-312
49
4
A:247-249
B:247-249
C:247-249
D:247-249
3
3
3
3
1.7
ENST00000299855
7
ENSE00001105439
chr11:
102709974-102709841
134
MMP3_HUMAN
312-357
46
0
-
-
1.8
ENST00000299855
8
ENSE00001801971
chr11:
102709441-102709282
160
MMP3_HUMAN
357-410
54
0
-
-
1.9
ENST00000299855
9
ENSE00001105448
chr11:
102708132-102708029
104
MMP3_HUMAN
410-445
36
0
-
-
1.11
ENST00000299855
11
ENSE00001292630
chr11:
102706957-102706532
426
MMP3_HUMAN
445-477
33
0
-
-
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1qica_ (A:)
1b: SCOP_d1qicb_ (B:)
1c: SCOP_d1qicc_ (C:)
1d: SCOP_d1qicd_ (D:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
Stromelysin-1 (MMP-3)
(40)
Human (Homo sapiens), fibroblast [TaxId: 9606]
(40)
1a
d1qica_
A:
1b
d1qicb_
B:
1c
d1qicc_
C:
1d
d1qicd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1qicA00 (A:89-249)
1b: CATH_1qicB00 (B:89-249)
1c: CATH_1qicC00 (C:89-249)
1d: CATH_1qicD00 (D:89-249)
View:
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)
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
1qicA00
A:89-249
1b
1qicB00
B:89-249
1c
1qicC00
C:89-249
1d
1qicD00
D:89-249
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_1qicD01 (D:91-247)
1b: PFAM_Peptidase_M10_1qicD02 (D:91-247)
1c: PFAM_Peptidase_M10_1qicD03 (D:91-247)
1d: PFAM_Peptidase_M10_1qicD04 (D:91-247)
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Clans
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)
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)
Organisms
(
)
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)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-1qicD01
D:91-247
1b
Peptidase_M10-1qicD02
D:91-247
1c
Peptidase_M10-1qicD03
D:91-247
1d
Peptidase_M10-1qicD04
D:91-247
[
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