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1Q3A
Biol. Unit 1
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
(1, 2)
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
-1
Ligand/Ion
CALCIUM ION
2
NGH
2
Ligand/Ion
N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYLHYDROXAMIC ACID
3
ZN
-1
Ligand/Ion
ZINC ION
[
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]
Sites
(13, 13)
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: BC7 (SOFTWARE)
12: BC8 (SOFTWARE)
13: 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
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
12
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
13
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
[
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]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_036139 (E142Q, chain A/B, )
2: VAR_MMP10_HUMAN_CCDS8321_1_01 (E142Q, chain A/B, )
3: VAR_020952 (F226L, chain A/B, )
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
E
142
Q
2
CancerSNP
VAR_MMP10_HUMAN_CCDS8321_1_01
*
E
142
Q
MMP10_HUMAN
Disease (Breast cancer)
---
A/B
E
142
Q
3
UniProt
VAR_020952
F
226
L
MMP10_HUMAN
Polymorphism
17860971
A/B
F
226
L
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:214-223,B: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
2
A:214-223
B:214-223
-
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1q3aa_ (A:)
1b: SCOP_d1q3ab_ (B:)
1c: SCOP_d1q3ac_ (C:)
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Protein Domains
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(
)
Organisms
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)
(
)
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:
[
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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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)
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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Clans
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(
)
Organisms
(
)
(
)
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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