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- Missing residues and incomplete sidechains (25,887 bytes)
18: ...sider [[Renumbering PDB files|renumbering the PDB file]].
96: ...download the AlphaFold model]. The downloaded PDB file can then be uploaded to [http://firstglance.jmol....
112: ...ivity with the substrates tested, the putative '''catalytic triad''' residues Thr2, Asp18, and Lys33 (UniProt...
113: ...e '''missing loops partially obscure the putative catalytic triad'''.
125: ...ket was removed in the image showing the putative catalytic triad.</ref>. {{Template:ColorKey_N2CRainbow}} - 1you (5,399 bytes)
2: ==Crystal structure of the catalytic domain of MMP-13 complexed with a potent pyrimidi...
26: ...gned based on a lead inhibitor identified through file screening. Incorporation of a biaryl ether moiety... - Sandbox UC 9 (2,556 bytes)
1: <Structure load='Insert PDB code or filename here' size='350' frame='true' align='right' c...
21: ...on|linear interpolation morph]]. The 14-model PDB file is [[Image:Morph-linear-1trh-1lpm.pdb.gz]].</ref>...
23: ...green'><b>LID</b></font>, <font color='orange'><b>catalytic triad: Ser209, Glu341, and His449</b></font><ref ...
26: ...ColorKey_Hydrophobic}} pocket is exposed with the catalytic triad in the bottom.
28: ...e:ColorKey_Hydrophobic}}, <font color='orange'><b>catalytic triad: Ser209, Glu341, and His449</b></font><ref ... - Sandbox Reserved 1692 (6,322 bytes)
7: ...y, I focused on the mutant H105F, which has a PDB file of 7ESN.
12: ...tom of Rha, suggesting these residues also play a catalytic role for the elimination reaction. <scene name='8... - Sandbox Reserved 1693 (6,581 bytes)
8: ... the mutant H105F Rha-GlcA ligand which has a PDB file: 7ESN. A colored image of this can be seen <scene...
18: ...lizing hydrogen bond with His 85, reinforcing the catalytic importance of His 85. The Rha Sugar cap on the GA...
20: ...lay an important role in stabilization during the catalytic mechanism. Ser170 and Pro223 Hbond with the O1 of...
29: ...uld not create a visualization of this as the PDB file places the acetate ion outside of the active site...
31: ...e site is important for substrate binding and the catalytic reaction, as the shape is determined by the amino... - 1ssc (4,653 bytes)
24: ...ections in the range 7.0-1.6 A (Protein Data Bank file ISSC). The structure is compared with the 2.0 A s... - Jmol/Cavities pockets and tunnels (22,245 bytes)
8: ...mol application]] and captured "cached" in a PNGJ file, which is then uploaded to Proteopedia for use in...
44: ...ill not work if the surface is loaded from a JVXL file alone, because then the surface has not been defi...
98: ...entrance, a pocket where substrate can access the catalytic site. The tunnel contains both NAD and a substrat...
124: ...which you start Jmol.jar. Any Jmol command script files should also be placed in this working directory....
126: ===Use PNGJ Files=== - Site (3,799 bytes)
1: ...tion (such as metal ions). Typical sites could be catalytic sites that bind substrates in enzymes, regulatory...
4: ...n, see under [https://www.wwpdb.org/documentation/file-format-content/format32/remarks2.html#REMARK%2080...
10: ...ence they will be absent in the atomic coordinate file. Thus, the absence of green links for ''Sites'' d...
12: ...al site was not included in the atomic coordinate file, it is relatively easy to add a green link that s... - Morphs (23,832 bytes)
15: ...] with a [[#True_Movies|true-movie]] morph of the catalytic reaction and conformational changes.
16: ...] with a [[#True_Movies|true-movie]] morph of the catalytic reaction and conformational changes.
54: ...onrhein'>Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Vonrhe...
71: ...ript commands while displaying the same morph PDB file.
75: ...r making true movies''' from multiple-model [[PDB files]], e.g. morphs, include: - Sandbox Reserved 713 (8,769 bytes)
54: ...tant metal to health. It acts as an indispensable catalytic and structural cofactor that drives many biologic...
65: [[Image:CuII coordination complex.jpg | thumb | 220px | left| Fig.2: Cu(I) binding geom...
81: ...[Image:Schematic representation of APP processing.jpg | thumb | 250px | right | fig 3 : Schematic repre...
91: .../www.rcsb.org/pdb/explore.do?structureId=2fkl PDB file of 2fkl] <br/>
92: .../www.rcsb.org/pdb/explore.do?structureId=2fk1 PDB file of 2fk1] <br/> - Sandbox Reserved 707 (16,400 bytes)
9: [[Image:1uwh bio r 500.jpg|left|300px|thumb| The complex of wild type B-RAF ...
16: [[Image:Reaction catalysed by raf protein family.jpg]]
25: ...520807</ref>. We have to say here that in the pdb file 1UWH the protein is already dimerized (as we will...
30: ... inferred interactions between human B-RAF kinase catalytic core residues, ATP, and MEK<ref>PMID:22569528</re...
33: ...name='Sandbox_Reserved_707/Active_site_of_1uwh/1'>catalytic site</scene><ref>PMID:3291115</ref> is just betwe... - Proteopedia:What's New (14,704 bytes)
40: * [[Eukaryotic Protein Kinase Catalytic Domain]]
85: ...is of specificity and a general properties of the catalytic mechanism
172: ...Pyruvate phosphate dikinase]] with a morph of the catalytic reaction and conformational changes.
173: ...r Phosphotransferase System]] with a morph of the catalytic reaction and conformational changes.
206: *[[Atomic coordinate file]] - User:Wayne Decatur (11,208 bytes)
1: ...pped smaller at Eileen Jewel performance 11-9-08..jpg|right|300px|Wayne Decatur in front row of Eilen J...
11: ...rotein complexes; the Ribosome; RNA modification; catalytic RNAs; homing endonucleases, group I introns; leuc...
44: ...LACED PDB ID CONTENT WITH OCA?!?!! I DID FInd the FILE FOR THE MORPH FOR THIS PAGE LISTED IN MY USER CON...
62: *[[Catalytic Molybdenum Metal-Organic Framework]]
71: *[[Getting Unremediated PDB Files]] - User:Max Lein/Sandbox (6,051 bytes)
5: ... may change the PDB parameter (which sets the PDB file loaded into the applet)
32: 3. Catalytic site that binds glycogen, Glc-1-P
33: 4. Inhibitor site, 12Å from catalytic site, binds caffeine and related compounds. - Complex III of Electron Transport Chain (15,482 bytes)
6: ... reactions of Complex III, but they do have other catalytic activities and functions. For the most part, the ...
9: ...10|ubiquinone]], and since it is empty in the PDB file, it is shown as <scene name='Complex_III_of_Elect...
13: ...s c, d, e, o, p, q) and their cofactors. The pdb file contains no substrates or inhibitors bound at Q<s...
31: ...urfaces/3'>Reset initial scene.</scene>) The PDB file used to generate the display has no cofactors bin... - Sandbox Z-DNA (10,455 bytes)
16: ...of double-stranded RNA binding motif (DRBM) and a catalytic domain related to ''E.coli'' cytidine deaminase....
32: <qt>file=Movie3_Z-DNA.mov|width=320|height=280|autoplay=fa... - Sandbox Z-DNA BindingProteins (5,860 bytes)
6: ...of double-stranded RNA binding motif (DRBM) and a catalytic domain related to ''E.coli'' cytidine deaminase....
22: <qt>file=Movie3_Z-DNA.mov|width=320|height=280|autoplay=fa... - 3ice (4,639 bytes)
24: ...video summary of this article, see the PaperFlick file with the Supplemental Data available online. - Intrinsically Disordered Protein (25,427 bytes)
27: ...ranges of amino acids with no [[atomic coordinate file|atomic coordinates]] in the model. These "ga...
70: ... and red is unfolded]]</td><td>[[Image:DisorderAA.jpg | thumb | Content of order-promoting and disorder...
147: ...the amino-terminal lobe and also inserts into the catalytic cleft, mimicking ATP. [[http://www.proteopedia.or... - Practical Guide to Homology Modeling (26,760 bytes)
31: ...ny of these methods, download the predicted [[PDB file]] and then upload it to [http://firstglance.jmol....
74: ...its, you will get the CIF file. If you need [[PDB file format]], click on the PDB ID code and open the '...
195: ...01'' (or 02, 03, etc.) and pick ''Download Linked File''.
216: ** Click on ''Upload your own PDB file'' and designate your homology model. Click ''View...
220: ...s lipases, e.g. [[1lpm]], where the pocket at the catalytic site is hydrophobic. Other exceptions would, of c...
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