Struct nom_pdb::secondary_structure::SsbondParser

pub struct SsbondParser;

SSBOND

The SSBOND record identifies each disulfide bond in protein and polypeptide structures by identifying the two residues involved in the bond.

The disulfide bond distance is included after the symmetry operations at the end of the SSBOND record.

Record Format

| COLUMNS | DATA TYPE | FIELD | DEFINITION | | ------- | ----------- | -------- | -------------------------------- | | 1 - 6 | Record name | "SSBOND" | | | 8 - 10 | Integer | serNum | Serial number. | | 12 - 14 | LString(3) | "CYS" | Residue name. | | 16 | Character | chainID1 | Chain identifier. | | 18 - 21 | Integer | seqNum1 | Residue sequence number. | | 22 | AChar | icode1 | Insertion code. | | 26 - 28 | LString(3) | "CYS" | Residue name. | | 30 | Character | chainID2 | Chain identifier. | | 32 - 35 | Integer | seqNum2 | Residue sequence number. | | 36 | AChar | icode2 | Insertion code. | | 60 - 65 | SymOP | sym1 | Symmetry operator for residue 1. | | 67 - 72 | SymOP | sym2 | Symmetry operator for residue 2. | | 74 – 78 | Real(5.2) | Length | Disulfide bond distance |

Details

• Bond distances between the sulfur atoms must be close to expected value.
• sym1 and sym2 are right justified and are always given even when identity operator (no cell translation) is to be applied to the residue.

Verification/Validation/Value Authority Control

wwPDB processing programs generate these records automatically.

Relationships to Other Record Types

CONECT records are generated for the disulfide bonds when SG atoms of both cysteines are present in the coordinate records.

Example

         1         2          3        4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
SSBOND   1 CYS A    6    CYS A  127                          1555   1555  2.03
SSBOND   2 CYS A   30    CYS A  115                          1555   1555  2.07
SSBOND   3 CYS A   64    CYS A   80                          1555   1555  2.06
SSBOND   4 CYS A   76    CYS A   94                          1555   1555  2.04

Known Problems

If SG of cysteine is disordered then there are possible alternate linkages. wwPDB practice is to put together all possible SSBOND records. This is problematic because the alternate location identifier is not specified in the SSBOND record.

Trait Implementations

impl FieldParser for SsbondParser

type Output = Ssbond

fn parse(inp: &[u8]) -> IResult<&[u8], Ssbond>

fn parse_into<'a, 'b>(inp: &'a [u8], dst: &'b mut Self::Output) -> &'a [u8]

fn parse_into_vec<'a>(inp: &'a [u8], dst: &mut Vec<Self::Output>) -> &'a [u8]

fn parse_into_option<'a>(
    inp: &'a [u8],
    dst: &mut Option<Self::Output>
) -> &'a [u8]