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Questions and answers > RNA structures (DSSR)
General questions of H-bond section in DSSR
lvelve0901:
Hi Xiangjun,
Sorry I gave a long list of questions yesterday. Here, I just post a few questions in terms of the H-bond in DSSR json.
For the H-bond between protein/peptide/ligand to nucleic acid, my target structure is 1PFE, which is a DNA bound to an antibiotic, echinomycin. I downloaded the biological assembly file and used the following command:
x3dna-dssr -i=1PFE.pdb -o=1PFE.json --json --more --symm
In the "hbonds" session of the output json file, I did found the all the DNA-drug interactions. For example,
{u'index': 31, u'atom2_serNum': 212, u'residue_pair': u'nt:aa', u'distance': 3.09, u'atom_pair': u'N:N', u'atom2_id': u'N@2:B.ALA6', u'donAcc_type': u'standard', u'atom1_id': u'N3@2:A.DG3', u'atom1_serNum': 69}
However, I have a few questions in terms of the hbonds output.
(1) How do I know which atom is H-bond donor and which is acceptor, like do you always put acceptor in the first place(atom1)?
(2) If the 'donAcc_type' is questionable, what does it mean? Does it mean that DSSR probably doesn't guess the valence properly?
(3) Wha does the 'serNum' mean here?
Here, I attached all my files.
Thank you.
Best,
Honglue
xiangjun:
--- Quote ---Sorry I gave a long list of questions yesterday. Here, I just post a few questions in terms of the H-bond in DSSR json.
--- End quote ---
Related questions are always welcome on the Forum. For ease of communication, just remember to keep each thread focused on a single topic, as you did here.
--- Quote ---{u'index': 31, u'atom2_serNum': 212, u'residue_pair': u'nt:aa', u'distance': 3.09, u'atom_pair': u'N:N', u'atom2_id': u'N@2:B.ALA6', u'donAcc_type': u'standard', u'atom1_id': u'N3@2:A.DG3', u'atom1_serNum': 69}
--- End quote ---
How did you get the above output for PDB id: 1PFE? Specifically, where does the 'u' before each tag name come from?
Using the following command, with jq (v1.5), the result seems clearer.
--- Code: ---# x3dna-dssr -i=1pfe.pdb --symm --get-hbond --json | jq .hbonds[30]
{
"index": 31,
"atom1_serNum": 69,
"atom2_serNum": 212,
"donAcc_type": "standard",
"distance": 3.09,
"atom1_id": "N3@2:A.DG3",
"atom2_id": "N@2:B.ALA6",
"atom_pair": "N:N",
"residue_pair": "nt:aa"
}
--- End code ---
--- Quote ---(1) How do I know which atom is H-bond donor and which is acceptor, like do you always put acceptor in the first place(atom1)?
(3) Wha does the 'serNum' mean here?
--- End quote ---
The list of H-bonds is ordered by atom serial numbers of the two H-bonding atoms. The atom serial number is taken from the corresponding PDB file. See the Coordinate Section, especially ATOM/HETATOM records of the documentation of the PDB format for details. The "toggle H-bonds" button in the DSSR-Jmol webpage takes advantage of this feature.
--- Quote ---(2) If the 'donAcc_type' is questionable, what does it mean? Does it mean that DSSR probably doesn't guess the valence properly?
--- End quote ---
It simply means DSSR cannot decide this is a donor-acceptor compatible H-bond, even though it fulfills the geometric criteria. It is up to the user to decide if this H-bond is feasible.
If you provide a concrete example, I may be able to give you more details on this topic.
HTH,
Xiang-Jun
lvelve0901:
Hi Xiangjun,
I have follow up questions in terms of donAcc_type in H-bond.
Here I attach the json output file of PDB 3BNQ. In the H-bond section, I see there are three types of donAcc_type: standard, acceptable and questionable. You have already explained to me what questionable mean but could you please explain the difference between standard and acceptable?
Also, is there anyway to tell which atom is donor and which atom is acceptor?
Thank you.
Best,
Honglue
xiangjun:
Could you please respond to my queries in answering your previous questions?
For your new questions, could you please post concrete examples to illustrate unambiguously what you mean? This is helpful not only for me and others to better understand you but also clarifies your own thought.
This Forum works best in a bidirectional conversation style instead of one-way Q&As.
Best regards,
Xiang-Jun
lvelve0901:
Hi Xiangjun,
Sorry I have been busy with other stuff in lab but I do remember your question last time.
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For your last question:
--- Quote from: xiangjun on November 02, 2017, 11:41:55 am ---
--- Quote ---{u'index': 31, u'atom2_serNum': 212, u'residue_pair': u'nt:aa', u'distance': 3.09, u'atom_pair': u'N:N', u'atom2_id': u'N@2:B.ALA6', u'donAcc_type': u'standard', u'atom1_id': u'N3@2:A.DG3', u'atom1_serNum': 69}
--- End quote ---
How did you get the above output for PDB id: 1PFE? Specifically, where does the 'u' before each tag name come from?
--- End quote ---
Basically, I just load the json use my way (my own json parser) and print out the 'hbonds' section. In my python, when I load the json file (using import json module), the string format will be loaded as unicode. I think that's why those string will have the 'u'. I think that is just my python string encode issue. Here is more explanation of the unicode string (https://stackoverflow.com/questions/21808657/what-is-a-unicode-string). I also tried your way as you suggested (using jq) but I didn't make it work. Do I need to install jq in my computer? I installed jq from the website
https://stedolan.github.io/jq/ and put the file in my working folder then type.
x3dna-dssr -i=3bnq.pdb --symm --get-hbond --json | jq . hbonds[1]
However, it outputs
Processing file '3bnq.pdb'
jq: error: Could not open file hbonds[1]: No such file or directory
I don't know if I did the right way.
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My new questions:
My new target structure is Mitochondrial Ribosomal Decoding Site (PDB ID: 3BNQ). I downloaded the PDB file (not biological assembly file) from RCSB. Then I try to generate the json file by typing:
x3dna-dssr -i=3bnq.pdb -o=3bnq.json --json --more --symm
I use my own json parser to look for the hydrogen bond between the RNA and the ligand PAR.
There are three examples with different don_Acc type here. All the hydrogen bonds mentioned below are labeled in the 3bnq.pse. Measure01 is the first example. Measure02 is the second example. Measure03 is the third example.
Example 1: Hbond index 117. donAcc_type acceptable.
{u'index': 117, u'atom2_serNum': 1928, u'residue_pair': u'nt:ligand', u'distance': 2.612, u'atom_pair': u'O:O', u'atom2_id': u'O41@C.PAR101', u'donAcc_type': u'acceptable', u'atom1_id': u'OP2@C.G22', u'atom1_serNum': 1426}
This is a hydrogen bond between a hydroxyl group in the ligand PAR and the OP2 atom in rG22.
Example 2: Hbond index 113. donAcc_type standard.
{u'index': 113, u'atom2_serNum': 1937, u'residue_pair': u'nt:ligand', u'distance': 2.63, u'atom_pair': u'O:N', u'atom2_id': u'N32@C.PAR101', u'donAcc_type': u'standard', u'atom1_id': u'OP2@C.C21', u'atom1_serNum': 1406}
This is a hydrogen bond between a amino group in the ligand PAR and the OP2 atom in rC21.
In both cases, it seems that the hydrogen bond geometry are very similar then why does the DSSR think they are different donAcc_type?
Example 3: Hbond index 107. donAcc_type questionable.
{u'index': 107, u'atom2_serNum': 1367, u'residue_pair': u'nt:nt', u'distance': 3.358, u'atom_pair': u'O:O', u'atom2_id': u"O4'@C.G19", u'donAcc_type': u'questionable', u'atom1_id': u"O4'@C.A17", u'atom1_serNum': 1323}
In this case, the DSSR identify a hbonds between two O4' atom, but we know that for ribose, the O4' is unlikely to be protonated. Is this the reason why DSSR think the donAcc_type is questionable?
I really appreciate your help.
Best,
Honglue
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
