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2W0D
Biol. Unit 2
Info
Asym.Unit (131 KB)
Biol.Unit 1 (34 KB)
Biol.Unit 2 (33 KB)
Biol.Unit 3 (33 KB)
Biol.Unit 4 (33 KB)
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(1)
Title
:
DOES A FAST NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY- AND X-RAY CRYSTALLOGRAPHY HYBRID APPROACH PROVIDE RELIABLE STRUCTURAL INFORMATION OF LIGAND-PROTEIN COMPLEXES? A CASE STUDY OF METALLOPROTEINASES.
Authors
:
J. Isaksson, S. Nystrom, D. J. Derbyshire, H. Wallberg, T. Agback, H. Ko I. Bertini, I. C. Felli
Date
:
13 Aug 08 (Deposition) - 03 Mar 09 (Release) - 28 Dec 11 (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
:
Glycoprotein, Metal-Binding, Metalloprotease, Secreted, Hydrolase, Hydroxamate, Extracellular Matrix, Copd, Mmp-12, Zymogen
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Isaksson, S. Nystrom, D. J. Derbyshire, H. Wallberg, T. Agback, H. Kovacs, I. Bertini, I. C. Felli
Does A Fast Nuclear Magnetic Resonance Spectroscopy- And X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information Of Ligand-Protein Complexes? A Case Study Of Metalloproteinases.
J. Med. Chem. V. 52 1712 2009
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
2i: CALCIUM ION (CAi)
2j: CALCIUM ION (CAj)
2k: CALCIUM ION (CAk)
2l: CALCIUM ION (CAl)
3a: N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)... (CGSa)
3b: N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)... (CGSb)
3c: N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)... (CGSc)
3d: N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)... (CGSd)
4a: CHLORIDE ION (CLa)
4b: CHLORIDE ION (CLb)
5a: SODIUM ION (NAa)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
6e: ZINC ION (ZNe)
6f: ZINC ION (ZNf)
6g: ZINC ION (ZNg)
6h: ZINC ION (ZNh)
6i: ZINC ION (ZNi)
6j: ZINC ION (ZNj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
-1
Ligand/Ion
ACETATE ION
2
CA
-1
Ligand/Ion
CALCIUM ION
3
CGS
1
Ligand/Ion
N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDEHYDROCHLORIDE
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
NA
-1
Ligand/Ion
SODIUM ION
6
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(7, 7)
Info
All Sites
1: AC6 (SOFTWARE)
2: AC7 (SOFTWARE)
3: AC8 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC1 (SOFTWARE)
6: DC3 (SOFTWARE)
7: DC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC6
SOFTWARE
HIS B:218 , HIS B:222 , HIS B:228 , CGS B:1269
BINDING SITE FOR RESIDUE ZN B1264
2
AC7
SOFTWARE
HIS B:168 , ASP B:170 , HIS B:183 , HIS B:196
BINDING SITE FOR RESIDUE ZN B1265
3
AC8
SOFTWARE
ASP B:175 , GLY B:176 , GLY B:178 , ILE B:180 , ASP B:198 , GLU B:201
BINDING SITE FOR RESIDUE CA B1266
4
AC9
SOFTWARE
ASP B:124 , GLU B:199 , GLU B:201 , HOH B:2111 , HOH B:2116
BINDING SITE FOR RESIDUE CA B1267
5
BC1
SOFTWARE
ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:2053 , HOH B:2099
BINDING SITE FOR RESIDUE CA B1268
6
DC3
SOFTWARE
ARG B:256 , ARG D:110 , HOH D:2009 , HOH D:2168 , HOH D:2169
BINDING SITE FOR RESIDUE ACT D1272
7
DC7
SOFTWARE
ILE B:180 , LEU B:181 , ALA B:182 , HIS B:218 , HIS B:222 , HIS B:228 , PRO B:238 , ZN B:1264 , HOH B:2168 , HOH B:2169 , HOH B:2170
BINDING SITE FOR RESIDUE CGS B1269
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (B:215-224)
;
View:
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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.
MMP12_HUMAN
215-224
1
-
B:215-224
-
-
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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, 4)
Info
All SCOP Domains
1a: SCOP_d2w0da_ (A:)
1b: SCOP_d2w0db_ (B:)
1c: SCOP_d2w0dc_ (C:)
1d: SCOP_d2w0dd_ (D:)
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Classes
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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
:
automated matches
(32)
Human (Homo sapiens) [TaxId: 9606]
(32)
1a
d2w0da_
A:
1b
d2w0db_
B:
1c
d2w0dc_
C:
1d
d2w0dd_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_2w0dD01 (D:108-263)
1b: PFAM_Peptidase_M10_2w0dD02 (D:108-263)
1c: PFAM_Peptidase_M10_2w0dD03 (D:108-263)
1d: PFAM_Peptidase_M10_2w0dD04 (D:108-263)
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Clans
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)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-2w0dD01
D:108-263
1b
Peptidase_M10-2w0dD02
D:108-263
1c
Peptidase_M10-2w0dD03
D:108-263
1d
Peptidase_M10-2w0dD04
D:108-263
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Chain B
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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Show PDB file:
Asym.Unit (131 KB)
Header - Asym.Unit
Biol.Unit 1 (34 KB)
Header - Biol.Unit 1
Biol.Unit 2 (33 KB)
Header - Biol.Unit 2
Biol.Unit 3 (33 KB)
Header - Biol.Unit 3
Biol.Unit 4 (33 KB)
Header - Biol.Unit 4
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