pdb-care: PDB CArbohydrate REsidue file check - description and examples


General information about this text:

The examples on this page show possible output of the pdb-care pdb file check software.
 For output excerpts, a monospace font is used.
 Informations are printed in black, warnings in blue and errors in red.
For explanation of the output, the standard font is used.


Output examples:

First of all, pdb-care checks the connections of HETATMs given in the CONECT tags of the pdb-file. Bond lengths outside a valid range or atoms whose valence is beyond the maximum number of connections allowed for the respective element are listed (excerpt from the output for PDB entry 1dzg):
 Distance check: Connection 3183-3194 (C-O) is 4.9. (expected: 1.1 - 1.7) ###

 Atom NAG_801L C2 (max. bonds: 4) is connected to 5 atoms: ASN_96L ND2, NAG_801L C1, NAG_801L C3, NAG_801L N2, NAG_801L O6

 Distance check: Connection 3245-3252 (C-N) is 66.6. (expected: 1.2 - 1.7) ###

 Distance check: Connection 6558-6566 (C-C) is 38.2. (expected: 1.2 - 1.8) ###

 Atom NAG_842I N2 (max. bonds: 4) is connected to 6 atoms: NAG_842I C2, NAG_842I C4, NAG_842I C7, NAG_842I N2, NAG_842I O3, NAG_861I C2

Afterwards, the residue names in the HETATM section of the pdb-file are checked for those where carbohydrate residues are to be expected (PDB entry 1gz9):
 check pdb residue names for carbohydrate rings to be expected:

    FUC 1559A: monosaccharide ?-?-Fucp

    LAT 1560A: lactose, 2 rings, linucs [][?-D-Glcp]{[(4+1)][b-D-Galp]{}}

 Expected number of carbohydrate rings from pdb residues: 3

In the next step the HETATMs are searched for potential carbohydrate rings, and the number of detected rings is displayed. For rings lacking an Oxygen or respective atom attached to the anomeric carbon, the software tries to assign connections to atoms in the vicinity of the anomeric carbon. In this case, a warnig message like
    Ring 1 (c1: 4368, NAG601A) assigned by c5-atom.
is displayed. If potential connections are found, they are listed below in the following form:
    Found 1 possible connection(s) for atom 4368:
    atom 729 (ASN92 ND2) dist.-dev. 0.032 score 1.123
The first number is the atom number in the pdb-file, followed by residue name, residue number and atom name. The next number shows the deviation of the bond distance from the average value, the last number contains a quality score derived from bond distance and bond angles (the lower, the better).


Subsequently, the detected carbohydrate rings are processed. For each ring, the residue name and number derived from the pdb-file and the position of the actual ring within the residue are displayed. The latter information is mainly interesting for oligsaccharide residues.
If the detected monosaccharide type does not match the one expected for the PDB residue, or the PDB residue is not yet implemented in the pdb-care software, an error or warning message is printed, and the program tries to suggest a better matching residue (e.g. pdb entry 1fce):
 #### PDB residue GLC 2101_  Ring 1/1 ####

 #### PDB residue GSC 2102_  Ring 1/0 ####

 Check PDB residue name: 'GSC'

 PDB residue name GSC not found in carbohydrate residue definition table, no check possible. ###

 PDB residue name(s) to use alternatively:

 SGC (b-D-Glcp4SH)

 GS4 (b-D-Glcp4SH)

 GSD (?-D-Glcp4SH)
In this example, most probably the first two letters of the name 'SGC' were interchanged, which results in a residue name unknown to pdb-care.

After an entire carbohydrate chain is processed, its LINUCS code is printed out (e.g. pdb entry 1axy, the LINUCS code is wrapped in this example to avoid horizontal scrolling of the explanatory texts; on the original page it appears in one line.):
 LINUCS: [][ASN]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}
           [(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}
           [(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}

To aid the user in reading the LINUCS code, it is printed again, this time with PDB residue information:
 LINUCS (+ PDB res.): [][ASN(ASN17)]{[(4+1)][b-D-GlcpNAc(NAG301)]{[(3+1)][a-L-Fucp(FUC302)]{}
                        [(4+1)][b-D-GlcpNAc(NAG303)]{[(4+1)][b-D-Manp(MAN304)]{[(2+1)][b-D-Xylp(XYS305)]{}
                        [(3+1)][a-D-Manp(MAN306)]{}[(6+1)][a-D-Manp(MAN307)]{}}}}}


In case the chain contains residues encoding for oligosaccharides (e.g. LAT: lactose) or combinations of carbohydrate- and non-carbohydrate parts (e.g. MFB: [][Me]{[(1+1)][b-L-Fucp]{}), a further check of the LINUCS code is performed to be able to test data beyond the monosaccharide information like linkages or the non-carbohydrate parts (example from pdb entry 1kwx: missing methyl group):
    PDB residue MFB 501G: LINUCS test mismatch:

       expected [][Me]{[(1+1)][b-L-Fucp]{*

       detected [][b-L-Fucp]{}



Finally, the PDB residues are reinspected to ensure that all carbohydrates were found. If expected carbohydrate residues were not assigned at all or the number of detected ring for a residue does not match the expected value, an error is displayed.
Failure of carbohydrate detection often results from missing connectivity information. Therefore, for these residues connections are determined by atom distances and probably missing connections are listed (example from pdb entry 1qk2):
    PDB resiue SGC 902A (expected rings: 1) was not assigned.

      (No rings detected)

      check for missing connections within residue SGC 902A:

        probably missing connection: 2867 ( C1 ) -> 2868 ( C2 ), distance 1.5 Å

        probably missing connection: 2867 ( C1 ) -> 2875 ( O5 ), distance 1.4 Å

        probably missing connection: 2868 ( C2 ) -> 2869 ( O2 ), distance 1.4 Å

        probably missing connection: 2868 ( C2 ) -> 2870 ( C3 ), distance 1.5 Å

        probably missing connection: 2870 ( C3 ) -> 2871 ( O3 ), distance 1.4 Å

        probably missing connection: 2870 ( C3 ) -> 2872 ( C4 ), distance 1.5 Å

        probably missing connection: 2872 ( C4 ) -> 2873 ( S4 ), distance 1.8 Å

        probably missing connection: 2872 ( C4 ) -> 2874 ( C5 ), distance 1.5 Å

        probably missing connection: 2874 ( C5 ) -> 2875 ( O5 ), distance 1.4 Å

        probably missing connection: 2874 ( C5 ) -> 2876 ( C6 ), distance 1.5 Å

        probably missing connection: 2876 ( C6 ) -> 2877 ( O6 ), distance 1.4 Å



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