Alternate locations of backbones: Difference between revisions
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4dgd X-ray diffraction 1.4 2012-01-25 min=0.03 ave 4.78 max 15.87 A=84 B=84 A.CA=13 B.CA=13 | 4dgd X-ray diffraction 1.4 2012-01-25 min=0.03 ave 4.78 max 15.87 A=84 B=84 A.CA=13 B.CA=13 | ||
* "Res" is the resolution in Å. | |||
* "Dep Date" is the date of deposition into the [[PDB]]. | |||
* min, ave, max are for the distances between AltLocs of '''backbone atoms only'''. "Backbone atoms" are protein alpha carbon atoms, and nucleic acid phosphorus atoms. | |||
* A and B are the AltLoc code characters used in these cases. Any alphanumeric characters are legal, and atoms may have more than two AltLocs. | |||
* The numbers after A= and B= are the numbers of atoms with A/B AltLoc codes. | |||
* The numbers after A.CA= and B.CA= are the numbers of alpha carbon atoms with A/B AltLoc codes. | |||
==Inter-AltLoc Backbone Distances== | ==Inter-AltLoc Backbone Distances== | ||
==AltLoc Backbone Cases== | ==AltLoc Backbone Cases== | ||
Revision as of 00:52, 8 June 2023
At sufficiently high resolution, empirical methods for determining macromolecular structure may detect multiple locations for some atoms, termed alternate locations. When alternate locations for backbones deviate substantially, the backbone may separate into two pathways ("fork") and then rejoin into a single pathway.
Alternate location serverAlternate location server
An Alternate Location Server (AltLoc Server) (part of the OCA Browser system) scans all entries in the Protein Data Bank, listing those that have alternate locations. The analysis below is based on an AltLoc Server report from late May, 2023, when the total number of entries in the PDB was ~200,700. Here are two example lines from the report:
ID Method Res Dep Date 9ins X-ray diffraction 1.70 1991-10-23 min=-1.0 ave=-1.0 max=-1.0 A=48 B=48 4dgd X-ray diffraction 1.4 2012-01-25 min=0.03 ave 4.78 max 15.87 A=84 B=84 A.CA=13 B.CA=13
- "Res" is the resolution in Å.
- "Dep Date" is the date of deposition into the PDB.
- min, ave, max are for the distances between AltLocs of backbone atoms only. "Backbone atoms" are protein alpha carbon atoms, and nucleic acid phosphorus atoms.
- A and B are the AltLoc code characters used in these cases. Any alphanumeric characters are legal, and atoms may have more than two AltLocs.
- The numbers after A= and B= are the numbers of atoms with A/B AltLoc codes.
- The numbers after A.CA= and B.CA= are the numbers of alpha carbon atoms with A/B AltLoc codes.