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1Q3A
Asym. Unit
Info
Asym.Unit (95 KB)
Biol.Unit 1 (60 KB)
Biol.Unit 2 (59 KB)
Biol.Unit 3 (31 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN MATRIX METALLOPROTEINASE 10
Authors
:
V. Calderone, I. Bertini, M. Fragai, C. Luchinat, S. Mangani, B. Terni
Date
:
29 Jul 03 (Deposition) - 06 Apr 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B (1x)
Biol. Unit 2: B,C (1x)
Biol. Unit 3: C (1x)
Keywords
:
Mmp-10, Metalloproteinase, Inhibitors, Nngh, Stromelysin-2, Hydroxamic Acid, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Bertini, V. Calderone, M. Fragai, C. Luchinat, S. Mangani, B. Terni
Crystal Structure Of The Catalytic Domain Of Human Matrix Metalloproteinase 10.
J. Mol. Biol. V. 336 707 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 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)
2a: N-ISOBUTYL-N-[4-METHOXYPHENYLSULFO... (NGHa)
2b: N-ISOBUTYL-N-[4-METHOXYPHENYLSULFO... (NGHb)
2c: N-ISOBUTYL-N-[4-METHOXYPHENYLSULFO... (NGHc)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
9
Ligand/Ion
CALCIUM ION
2
NGH
3
Ligand/Ion
N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYLHYDROXAMIC ACID
3
ZN
6
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
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:217 , HIS A:221 , HIS A:227 , NGH A:480
BINDING SITE FOR RESIDUE ZN A 464
02
AC2
SOFTWARE
HIS A:167 , ASP A:169 , HIS A:182 , HIS A:195
BINDING SITE FOR RESIDUE ZN A 465
03
AC3
SOFTWARE
ASP A:174 , GLY A:175 , GLY A:177 , SER A:179 , ASP A:197 , GLU A:200
BINDING SITE FOR RESIDUE CA A 466
04
AC4
SOFTWARE
ASP A:157 , GLY A:189 , TYR A:191 , ASP A:193
BINDING SITE FOR RESIDUE CA A 467
05
AC5
SOFTWARE
ASP A:123 , ASP A:198 , GLU A:200 , HOH A:564 , HOH A:597
BINDING SITE FOR RESIDUE CA A 468
06
AC6
SOFTWARE
HIS B:217 , HIS B:221 , HIS B:227 , NGH B:479
BINDING SITE FOR RESIDUE ZN B 469
07
AC7
SOFTWARE
HIS B:167 , ASP B:169 , HIS B:182 , HIS B:195
BINDING SITE FOR RESIDUE ZN B 470
08
AC8
SOFTWARE
ASP B:174 , GLY B:175 , GLY B:177 , SER B:179 , ASP B:197 , GLU B:200
BINDING SITE FOR RESIDUE CA B 471
09
AC9
SOFTWARE
ASP B:157 , GLY B:189 , TYR B:191 , ASP B:193 , HOH B:513
BINDING SITE FOR RESIDUE CA B 472
10
BC1
SOFTWARE
ASP B:123 , ASP B:198 , GLU B:200 , HOH B:482 , HOH B:500
BINDING SITE FOR RESIDUE CA B 473
11
BC2
SOFTWARE
HIS C:217 , HIS C:221 , HIS C:227 , NGH C:481 , HOH C:491
BINDING SITE FOR RESIDUE ZN C 474
12
BC3
SOFTWARE
HIS C:167 , ASP C:169 , HIS C:182 , HIS C:195
BINDING SITE FOR RESIDUE ZN C 475
13
BC4
SOFTWARE
ASP C:174 , GLY C:175 , GLY C:177 , SER C:179 , ASP C:197 , GLU C:200
BINDING SITE FOR RESIDUE CA C 476
14
BC5
SOFTWARE
ASP C:157 , GLY C:189 , TYR C:191 , ASP C:193 , HOH C:498
BINDING SITE FOR RESIDUE CA C 477
15
BC6
SOFTWARE
ASP C:123 , ASP C:198 , GLU C:200
BINDING SITE FOR RESIDUE CA C 478
16
BC7
SOFTWARE
SER B:179 , LEU B:180 , ALA B:181 , LEU B:213 , HIS B:217 , GLU B:218 , HIS B:221 , HIS B:227 , PRO B:237 , TYR B:239 , ZN B:469 , HOH B:583 , HIS C:178
BINDING SITE FOR RESIDUE NGH B 479
17
BC8
SOFTWARE
HIS A:178 , SER A:179 , LEU A:180 , ALA A:181 , LEU A:213 , HIS A:217 , GLU A:218 , HIS A:221 , HIS A:227 , PRO A:237 , SER A:241 , ZN A:464 , HOH A:485 , HOH A:612 , HIS B:178
BINDING SITE FOR RESIDUE NGH A 480
18
BC9
SOFTWARE
ASN B:240 , PHE B:242 , HOH B:499 , HOH B:535 , HOH B:605 , SER C:179 , LEU C:180 , ALA C:181 , HIS C:217 , GLU C:218 , HIS C:221 , HIS C:227 , LEU C:234 , LEU C:238 , TYR C:239 , ZN C:474 , HOH C:491 , HOH C:504 , HOH C:517 , HOH C:520 , HOH C:544
BINDING SITE FOR RESIDUE NGH C 481
[
close Site info
]
SAPs(SNPs)/Variants
(3, 9)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_036139 (E142Q, chain A/B/C, )
2: VAR_MMP10_HUMAN_CCDS8321_1_01 (E142Q, chain A/B/C, )
3: VAR_020952 (F226L, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_036139
E
142
Q
MMP10_HUMAN
Unclassified
---
A/B/C
E
142
Q
2
CancerSNP
VAR_MMP10_HUMAN_CCDS8321_1_01
*
E
142
Q
MMP10_HUMAN
Disease (Breast cancer)
---
A/B/C
E
142
Q
3
UniProt
VAR_020952
F
226
L
MMP10_HUMAN
Polymorphism
17860971
A/B/C
F
226
L
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:214-223,B:214-223,C:214-223)
;
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.
MMP10_HUMAN
214-223
3
A:214-223
B:214-223
C:214-223
[
close PROSITE info
]
Exons
(5, 15)
Info
All Exons
Exon 1.2 (A:105-116 | B:104-116 | C:106-116)
Exon 1.3 (A:116-166 | B:116-166 | C:116-166)
Exon 1.4 (A:166-208 | B:166-208 | C:166-208)
Exon 1.5 (A:208-263 (gaps) | B:208-263 | C:2...)
Exon 1.6 (A:263-263 | B:263-263 | C:263-263)
View:
Select:
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All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
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
1.1
ENST00000279441
1
ENSE00000993214
chr11:
102651359-102651218
142
MMP10_HUMAN
1-35
35
0
-
-
1.2
ENST00000279441
2
ENSE00000993200
chr11:
102650476-102650235
242
MMP10_HUMAN
36-116
81
3
A:105-116
B:104-116
C:106-116
12
13
11
1.3
ENST00000279441
3
ENSE00001758252
chr11:
102650092-102649944
149
MMP10_HUMAN
116-166
51
3
A:116-166
B:116-166
C:116-166
51
51
51
1.4
ENST00000279441
4
ENSE00000993192
chr11:
102649480-102649355
126
MMP10_HUMAN
166-208
43
3
A:166-208
B:166-208
C:166-208
43
43
43
1.5
ENST00000279441
5
ENSE00001706030
chr11:
102647507-102647343
165
MMP10_HUMAN
208-263
56
3
A:208-263 (gaps)
B:208-263
C:208-263 (gaps)
56
56
56
1.6
ENST00000279441
6
ENSE00000993219
chr11:
102647155-102647011
145
MMP10_HUMAN
263-311
49
3
A:263-263
B:263-263
C:263-263
1
1
1
1.7
ENST00000279441
7
ENSE00000993209
chr11:
102646052-102645919
134
MMP10_HUMAN
311-356
46
0
-
-
1.8
ENST00000279441
8
ENSE00001692235
chr11:
102643737-102643578
160
MMP10_HUMAN
356-409
54
0
-
-
1.9
ENST00000279441
9
ENSE00000993181
chr11:
102642846-102642743
104
MMP10_HUMAN
409-444
36
0
-
-
1.10
ENST00000279441
10
ENSE00000993208
chr11:
102641624-102641245
380
MMP10_HUMAN
444-476
33
0
-
-
[
close EXON info
]
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1q3aa_ (A:)
1b: SCOP_d1q3ab_ (B:)
1c: SCOP_d1q3ac_ (C:)
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)
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)
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)
(
)
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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-2 (MMP-10)
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1q3aa_
A:
1b
d1q3ab_
B:
1c
d1q3ac_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1q3aB00 (B:104-263)
1b: CATH_1q3aA00 (A:105-263)
1c: CATH_1q3aC00 (C:106-263)
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(
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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
1q3aB00
B:104-263
1b
1q3aA00
A:105-263
1c
1q3aC00
C:106-263
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_1q3aC01 (C:107-263)
1b: PFAM_Peptidase_M10_1q3aC02 (C:107-263)
1c: PFAM_Peptidase_M10_1q3aC03 (C:107-263)
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)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-1q3aC01
C:107-263
1b
Peptidase_M10-1q3aC02
C:107-263
1c
Peptidase_M10-1q3aC03
C:107-263
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]
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