Alternate locations of backbones - Revision history

Eric Martz: /* Case 1: Flexible active site loop broadens range of protection. */

2023-08-13T23:48:26Z

Case 1: Flexible active site loop broadens range of protection.

←Older revision		Revision as of 23:48, 13 August 2023
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	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
-	\| [https://www.uniprot.org/uniprotkb/B0LJC8/entry TRIMCyp protein] mediates innate immunity to HIV by inhibiting post-entry retrovirus replication. Evidence suggests that TRIMCyp has evolved through mutations to broaden the range of retroviruses it can inhibit<ref name="4dgd">PMID: 22407016</ref>. These mutations render the active site able to assume multiple conformations. In particular, the cyclophilin-binding loop 64-74 (GGNFT HCNGT GG), flanked by double glycine pivots, exhibited flexibility<ref name="4dgd" />. A crystal structure, [[4dgd]], resolved two alternate location conformations for the loop residues 66-74, shown at right in red (AltLoc A) and orange (AltLoc B), each at about 50% occupancy.	+	\| [https://www.uniprot.org/uniprotkb/B0LJC8/entry TRIMCyp protein] mediates innate immunity to HIV by inhibiting post-entry retrovirus replication. Evidence suggests that TRIMCyp has evolved through mutations to broaden the range of retroviruses it can inhibit<ref name="4dgd">PMID: 22407016</ref>. These mutations render the active site able to assume multiple conformations. In particular, the cyclophilin-binding loop 64-74 (GGNFT HCNGT GG), flanked by double glycine pivots, exhibited flexibility<ref name="4dgd" />. A crystal structure, [[4dgd]], resolved two alternate location conformations for the loop residues 66-74, shown at right in '''{{Font color\|red\|red (AltLoc A)}}''' and '''{{Font color\|orange\|orange (AltLoc B)}}''', each at about 50% occupancy.

	Explore [http://firstglance.jmol.org/fg.htm?mol=4dgd 4DGD in FirstGlance in Jmol], which has [[Alternate_locations#Visualizing_alternate_locations\|AltLoc visualization/animation capabilities]].		Explore [http://firstglance.jmol.org/fg.htm?mol=4dgd 4DGD in FirstGlance in Jmol], which has [[Alternate_locations#Visualizing_alternate_locations\|AltLoc visualization/animation capabilities]].

Eric Martz: /* X-ray diffraction */

2023-07-29T16:50:36Z

X-ray diffraction

←Older revision		Revision as of 16:50, 29 July 2023
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	<!--However, not quite ~500 entries (<1%) have "substantial" separations of some AltLoc backbone atoms, namely separations averaging >2.5 Å.-->		<!--However, not quite ~500 entries (<1%) have "substantial" separations of some AltLoc backbone atoms, namely separations averaging >2.5 Å.-->
	(The [[van der Waals radii\|van der Waals diameter]] of a carbon atom is 3.4 Å.		(The [[van der Waals radii\|van der Waals diameter]] of a carbon atom is 3.4 Å.
-	The '''average''' separations for those 1,035 with maximum separations >5.0 Å range from 0.14 to 91 Å, with 184 entries having average separations >5.0 Å.) 3,560 entries have maximum separations ≥2.0 &Aring, and 6,125 ≥ 1.0 Å.	+	The '''average''' separations for those 1,035 with maximum separations >5.0 Å range from 0.14 to 91 Å, with 184 entries having average separations >5.0 Å.) 3,560 entries have maximum separations ≥2.0 Å, and 6,125 ≥ 1.0 Å.

	{\| class="wikitable"		{\| class="wikitable"

Eric Martz: /* X-ray diffraction */

2023-07-29T16:49:51Z

X-ray diffraction

←Older revision		Revision as of 16:49, 29 July 2023
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	<!--However, not quite ~500 entries (<1%) have "substantial" separations of some AltLoc backbone atoms, namely separations averaging >2.5 Å.-->		<!--However, not quite ~500 entries (<1%) have "substantial" separations of some AltLoc backbone atoms, namely separations averaging >2.5 Å.-->
	(The [[van der Waals radii\|van der Waals diameter]] of a carbon atom is 3.4 Å.		(The [[van der Waals radii\|van der Waals diameter]] of a carbon atom is 3.4 Å.
-	The '''average''' separations for those 1,035 with maximum separations >5.0 Å range from 0.14 to 91 Å, with 184 entries having average separations >5.0 Å.)	+	The '''average''' separations for those 1,035 with maximum separations >5.0 Å range from 0.14 to 91 Å, with 184 entries having average separations >5.0 Å.) 3,560 entries have maximum separations ≥2.0 &Aring, and 6,125 ≥ 1.0 Å.

	{\| class="wikitable"		{\| class="wikitable"

Eric Martz: /* Additional Cases */

2023-07-08T20:31:49Z

Additional Cases

←Older revision		Revision as of 20:31, 8 July 2023
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	* [http://firstglance.jmol.org/fg.htm?mol=3pga 3PGA], a glutaminase-asparaginase, has a 20-residue flexible loop that is thought to orient substrate and help to transport substrate and product from the active site.		* [http://firstglance.jmol.org/fg.htm?mol=3pga 3PGA], a glutaminase-asparaginase, has a 20-residue flexible loop that is thought to orient substrate and help to transport substrate and product from the active site.

-	* [http://firstglance.jmol.org/fg.htm?mol=~~3qku 3QKU~~] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).	+	* [http://firstglance.jmol.org/fg.htm?mol=3kqu 3KQU] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).

	* The [http://firstglance.jmol.org/fg.htm?mol=4myd&au=1 asymmetric unit of 4MYD] is a trimeric enzyme, in which "two [chains] bind one or both small molecule ligands and the third in the middle is present in two C2-symmetric conformations in a 1:1 ratio without any ligands." Here you will see alternate locations representing the entire middle chain rotated close to 180 degrees.		* The [http://firstglance.jmol.org/fg.htm?mol=4myd&au=1 asymmetric unit of 4MYD] is a trimeric enzyme, in which "two [chains] bind one or both small molecule ligands and the third in the middle is present in two C2-symmetric conformations in a 1:1 ratio without any ligands." Here you will see alternate locations representing the entire middle chain rotated close to 180 degrees.

Eric Martz: /* Additional Cases */

2023-07-06T22:03:50Z

Additional Cases

←Older revision		Revision as of 22:03, 6 July 2023
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	* The [http://firstglance.jmol.org/fg.htm?mol=4myd&au=1 asymmetric unit of 4MYD] is a trimeric enzyme, in which "two [chains] bind one or both small molecule ligands and the third in the middle is present in two C2-symmetric conformations in a 1:1 ratio without any ligands." Here you will see alternate locations representing the entire middle chain rotated close to 180 degrees.		* The [http://firstglance.jmol.org/fg.htm?mol=4myd&au=1 asymmetric unit of 4MYD] is a trimeric enzyme, in which "two [chains] bind one or both small molecule ligands and the third in the middle is present in two C2-symmetric conformations in a 1:1 ratio without any ligands." Here you will see alternate locations representing the entire middle chain rotated close to 180 degrees.
		+
		+	* [http://firstglance.jmol.org/fg.htm?mol=6xkc 6XKC] is a hexamer. Two of the chains are modeled at two different angles relative to the other 4. In animation, these chains wave back and forth.

	==References==		==References==
	<references />		<references />

Eric Martz: /* Additional Cases */

2023-07-06T21:30:02Z

Additional Cases

←Older revision		Revision as of 21:30, 6 July 2023
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	====Additional Cases====		====Additional Cases====
		+
		+
		+	* [http://firstglance.jmol.org/fg.htm?mol=3pga 3PGA], a glutaminase-asparaginase, has a 20-residue flexible loop that is thought to orient substrate and help to transport substrate and product from the active site.

	* [http://firstglance.jmol.org/fg.htm?mol=3qku 3QKU] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).		* [http://firstglance.jmol.org/fg.htm?mol=3qku 3QKU] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).

Eric Martz: /* Additional Cases */

2023-07-06T21:20:16Z

Additional Cases

←Older revision		Revision as of 21:20, 6 July 2023
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	* [http://firstglance.jmol.org/fg.htm?mol=3qku 3QKU] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).		* [http://firstglance.jmol.org/fg.htm?mol=3qku 3QKU] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).

-	* The [http://firstglance.jmol.org/fg.htm?mol=4myd&au=1 asymmetric unit of 4MYD] is a trimeric enzyme, in which "two [chains] bind one or both small molecule ligands and the third in the middle is present in two C2-symmetric conformations in a 1:1 ratio without any ligands." Here you will see the entire middle chain rotated close to 180 degrees.	+	* The [http://firstglance.jmol.org/fg.htm?mol=4myd&au=1 asymmetric unit of 4MYD] is a trimeric enzyme, in which "two [chains] bind one or both small molecule ligands and the third in the middle is present in two C2-symmetric conformations in a 1:1 ratio without any ligands." Here you will see alternate locations representing the entire middle chain rotated close to 180 degrees.

	==References==		==References==
	<references />		<references />

Eric Martz: /* Additional Cases */

2023-07-06T21:19:45Z

Additional Cases

←Older revision		Revision as of 21:19, 6 July 2023
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	* [http://firstglance.jmol.org/fg.htm?mol=3qku 3QKU] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).		* [http://firstglance.jmol.org/fg.htm?mol=3qku 3QKU] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).

-	* [http://firstglance.jmol.org/fg.htm?mol=4myd&au=1 ~~4MYD]'s~~ asymmetric unit is a trimeric enzyme, in which "two [chains] bind one or both small molecule ligands and the third in the middle is present in two C2-symmetric conformations in a 1:1 ratio without any ligands." Here you will see the entire middle chain rotated close to 180 degrees.	+	* The [http://firstglance.jmol.org/fg.htm?mol=4myd&au=1 asymmetric unit of 4MYD] is a trimeric enzyme, in which "two [chains] bind one or both small molecule ligands and the third in the middle is present in two C2-symmetric conformations in a 1:1 ratio without any ligands." Here you will see the entire middle chain rotated close to 180 degrees.

	==References==		==References==
	<references />		<references />

Eric Martz: /* Additional Cases */

2023-07-06T21:18:37Z

Additional Cases

←Older revision		Revision as of 21:18, 6 July 2023
Line 151:		Line 151:

	* [http://firstglance.jmol.org/fg.htm?mol=3qku 3QKU] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).		* [http://firstglance.jmol.org/fg.htm?mol=3qku 3QKU] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).
		+
		+	* [http://firstglance.jmol.org/fg.htm?mol=4myd&au=1 4MYD]'s asymmetric unit is a trimeric enzyme, in which "two [chains] bind one or both small molecule ligands and the third in the middle is present in two C2-symmetric conformations in a 1:1 ratio without any ligands." Here you will see the entire middle chain rotated close to 180 degrees.

	==References==		==References==
	<references />		<references />

Eric Martz: /* Additional Cases */

2023-07-06T20:21:38Z

Additional Cases

←Older revision		Revision as of 20:21, 6 July 2023
Line 149:		Line 149:

	====Additional Cases====		====Additional Cases====
		+
		+	* [http://firstglance.jmol.org/fg.htm?mol=3qku 3QKU] illustrates a helicase ratchet translocation mechanism with its single-stranded DNA in four positions (conformations).

	==References==		==References==
	<references />		<references />