Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

YDP

Bonds
First atomSecond atomBond order typeDistance
(experimental model)
Distance
(ideal model)
Properties
N1C8sing1.35Å1.36Å
C5C6doub1.40Å1.40ÅAromatic
C5C20sing1.38Å1.40ÅAromatic
C6C8sing1.48Å1.52Å
C6C2sing1.40Å1.40ÅAromatic
C8O2doub1.22Å1.22Å
C10C35sing1.51Å1.51Å
C20C27doub1.38Å1.40ÅAromatic
C24N32sing1.46Å1.47Å
C24C25sing1.54Å1.55Å
C24C23sing1.55Å1.55Å
C27C18sing1.38Å1.40ÅAromatic
C27S9sing1.76Å1.78Å
C18C2doub1.38Å1.40ÅAromatic
S9O40doub1.42Å1.45Å
S9N32sing1.66Å1.73Å
S9O11doub1.42Å1.45Å
N32C33sing1.47Å1.46Å
C33C34sing1.51Å1.51Å
C34C35doub1.31Å1.35Å
C35C11sing1.51Å1.51Å
C25N22sing1.48Å1.47Å
N22C26sing1.49Å1.47Å
N2C9sing1.35Å1.36Å
C3C4doub1.40Å1.40ÅAromatic
C3C19sing1.38Å1.40ÅAromatic
O3C9doub1.22Å1.22Å
C7C4sing1.40Å1.40ÅAromatic
C7C21doub1.38Å1.40ÅAromatic
C4C9sing1.48Å1.52Å
S10O12doub1.42Å1.45Å
S10C28sing1.76Å1.78Å
S10N36sing1.66Å1.73Å
S10O41doub1.42Å1.45Å
C12C39sing1.51Å1.51Å
C13C39sing1.51Å1.51Å
C19C28doub1.38Å1.40ÅAromatic
C21C28sing1.38Å1.39ÅAromatic
C23C26sing1.55Å1.55Å
C23N36sing1.47Å1.47Å
N36C37sing1.46Å1.46Å
C37C38sing1.51Å1.51Å
C38C39doub1.31Å1.35Å
N1HN1sing0.97Å1.00Å
N1HN1Asing0.97Å1.00Å
C5H5sing1.08Å1.08Å
C10H10sing1.09Å1.10Å
C10H10Asing1.09Å1.10Å
C10H10Bsing1.09Å1.10Å
C20H20sing1.08Å1.08Å
C24H24sing1.09Å1.10Å
C18H18sing1.08Å1.08Å
C2H2sing1.08Å1.08Å
C33H33sing1.09Å1.10Å
C33H33Asing1.09Å1.10Å
C34H34sing1.08Å1.08Å
C11H11sing1.09Å1.10Å
C11H11Asing1.09Å1.10Å
C11H11Bsing1.09Å1.10Å
C25H25sing1.09Å1.10Å
C25H25Asing1.09Å1.10Å
N22HN22sing1.01Å1.00Å
N2HN2sing0.97Å1.00Å
N2HN2Asing0.97Å1.00Å
C3H3sing1.08Å1.08Å
C7H7sing1.08Å1.08Å
C12H12sing1.09Å1.10Å
C12H12Asing1.09Å1.10Å
C12H12Bsing1.09Å1.10Å
C13H13sing1.09Å1.10Å
C13H13Asing1.09Å1.10Å
C13H13Bsing1.09Å1.10Å
C19H19sing1.08Å1.08Å
C21H21sing1.08Å1.08Å
C23H23sing1.09Å1.10Å
C26H26sing1.09Å1.10Å
C26H26Asing1.09Å1.10Å
C37H37sing1.09Å1.10Å
C37H37Asing1.09Å1.10Å
C38H38sing1.08Å1.08Å
Angles
First atomSecond atomThird atomAngle
(experimental model)
Angle
(ideal model)
N1C8C6120.7°120.0°
N1C8O2120.1°120.0°
C8N1HN1108.0°120.0°
C8N1HN1A126.0°120.0°
C6C5C20121.9°119.9°
C5C6C8122.2°120.2°
C5C6C2118.8°119.7°
C6C5H5119.1°120.1°
C5C20C27119.0°120.1°
C20C5H5119.1°120.1°
C5C20H20120.5°119.9°
C8C6C2118.9°120.2°
C6C8O2118.8°120.0°
C6C2C18119.3°119.9°
C6C2H2120.3°120.0°
C10C35C34118.5°120.0°
C10C35C11116.2°120.0°
C35C10H10109.5°109.5°
C35C10H10A109.5°109.4°
C35C10H10B109.5°109.5°
C20C27C18119.4°120.4°
C20C27S9120.8°119.8°
C27C20H20120.5°120.0°
N32C24C25116.2°110.3°
N32C24C23115.5°110.4°
C24N32S9115.8°120.0°
C24N32C33126.0°120.0°
N32C24H2498.2°110.2°
C25C24C23103.6°105.2°
C24C25N22106.4°107.0°
C25C24H24111.4°110.3°
C24C25H25110.5°109.9°
C24C25H25A111.2°109.9°
C24C23C26103.6°103.0°
C24C23N36115.6°110.7°
C23C24H24112.2°110.4°
C24C23H23112.2°110.7°
C18C27S9119.8°119.8°
C27C18C2121.6°120.1°
C27C18H18119.2°120.0°
C27S9O40106.4°106.4°
C27S9N32104.3°107.2°
C27S9O11105.7°106.4°
C2C18H18119.2°119.9°
C18C2H2120.3°120.1°
O40S9N32109.5°106.4°
O40S9O11123.0°123.2°
N32S9O11106.3°106.3°
S9N32C33118.2°120.0°
N32C33C34116.7°109.4°
N32C33H33107.1°109.5°
N32C33H33A105.5°109.5°
C33C34C35125.8°120.0°
C34C33H33107.2°109.5°
C34C33H33A105.5°109.4°
C33C34H34117.1°120.0°
C34C35C11125.3°120.0°
C35C34H34117.1°120.0°
C35C11H11109.5°109.4°
C35C11H11A109.4°109.5°
C35C11H11B109.5°109.4°
C25N22C26110.1°105.8°
N22C25H25110.5°109.9°
N22C25H25A111.1°109.9°
C25N22HN22109.2°111.0°
N22C26C23106.4°103.2°
C26N22HN22109.3°111.0°
N22C26H26110.5°110.7°
N22C26H26A111.2°110.7°
N2C9O3120.2°120.1°
N2C9C4120.7°120.0°
C9N2HN2112.0°120.0°
C9N2HN2A124.0°120.1°
C4C3C19119.4°119.9°
C3C4C7118.8°119.7°
C3C4C9119.0°120.2°
C4C3H3120.3°120.1°
C3C19C28121.6°120.1°
C19C3H3120.3°120.1°
C3C19H19119.2°119.9°
O3C9C4118.8°119.9°
C4C7C21121.8°119.9°
C7C4C9122.2°120.2°
C4C7H7119.1°120.0°
C7C21C28119.0°120.1°
C21C7H7119.1°120.1°
C7C21H21120.5°119.9°
O12S10C28105.7°106.4°
O12S10N36106.3°106.4°
O12S10O41123.0°123.1°
C28S10N36104.3°107.2°
C28S10O41106.4°106.4°
S10C28C19119.8°119.8°
S10C28C21120.8°119.9°
N36S10O41109.5°106.4°
S10N36C23115.8°120.0°
S10N36C37118.2°120.0°
C12C39C13116.2°120.0°
C12C39C38118.5°120.0°
C39C12H12109.5°109.5°
C39C12H12A109.5°109.5°
C39C12H12B109.5°109.5°
C13C39C38125.3°119.9°
C39C13H13109.5°109.4°
C39C13H13A109.5°109.5°
C39C13H13B109.5°109.5°
C19C28C21119.4°120.3°
C28C19H19119.2°120.0°
C28C21H21120.5°119.9°
C26C23N36116.2°110.7°
C26C23H23111.4°110.7°
C23C26H26110.5°110.6°
C23C26H26A111.2°110.7°
C23N36C37126.0°120.0°
N36C23H2398.2°110.8°
N36C37C38116.7°109.5°
N36C37H37107.1°109.4°
N36C37H37A105.5°109.5°
C37C38C39125.9°119.9°
C38C37H37107.2°109.5°
C38C37H37A105.5°109.5°
C37C38H38117.1°120.0°
C39C38H38117.1°120.1°
HN1N1HN1A126.0°120.0°
H10C10H10A109.4°109.4°
H10C10H10B109.5°109.5°
H10AC10H10B109.5°109.4°
H33C33H33A115.3°109.5°
H11C11H11A109.5°109.5°
H11C11H11B109.4°109.4°
H11AC11H11B109.5°109.5°
H25C25H25A107.2°110.1°
HN2N2HN2A124.0°119.9°
H12C12H12A109.5°109.5°
H12C12H12B109.4°109.5°
H12AC12H12B109.5°109.5°
H13C13H13A109.5°109.4°
H13C13H13B109.5°109.5°
H13AC13H13B109.4°109.5°
H26C26H26A107.1°110.7°
H37C37H37A115.3°109.5°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)
Torsion
(ideal model)
N1C8C6C52.7°174.6°
N1C8C6O2173.8°180.0°
N1C8C6C2177.6°5.4°
C8N1HN1HN1A180.0°179.6°
C6C5C20H5180.0°179.7°
C5C6C8C2179.7°180.0°
C5C6C8O2176.5°5.5°
C6C5C20C271.3°0.0°
C5C6C2C181.5°0.0°
C6C5C20H20178.6°179.9°
C5C6C2H2178.5°180.0°
C20C5C6C8177.8°180.0°
C20C5C6C21.9°0.0°
C5C20C27H20180.0°179.9°
C5C20C27C180.3°0.0°
C5C20C27S9179.5°180.0°
C8C6C2C18178.3°180.0°
C6C8N1HN10.0°5.0°
C6C8N1HN1A180.0°174.7°
C8C6C5H52.2°0.3°
C8C6C2H21.7°0.0°
C2C6C8O23.8°174.6°
C6C2C18C270.5°0.0°
C6C2C18H2180.0°180.0°
C2C6C5H5178.1°179.7°
C6C2C18H18179.5°179.9°
O2C8N1HN1173.7°175.0°
O2C8N1HN1A6.3°5.3°
C10C35C34C33177.9°0.0°
C10C35C34C11179.2°180.0°
C35C10H10H10A120.0°119.9°
C35C10H10H10B120.0°120.1°
C35C10H10AH10B120.0°120.0°
C10C35C34H342.0°180.0°
C10C35C11H113.9°89.9°
C10C35C11H11A116.1°150.0°
C10C35C11H11B123.9°30.0°
C20C27C18S9179.8°180.0°
C20C27C18C20.1°0.1°
C20C27S9O403.0°29.0°
C20C27S9N32118.8°84.5°
C20C27S9O11129.3°162.0°
C27C20C5H5178.7°179.7°
C20C27C18H18179.9°179.9°
N32C24C25C23127.9°119.0°
N32C24C25H24111.4°122.0°
N32C24C23H24111.5°122.1°
C24N32S9C2793.9°97.2°
C24N32S9O40152.5°149.3°
C24N32S9C33178.7°180.0°
C24N32S9O1117.5°16.3°
C24N32C33C3490.7°85.3°
N32C24C25N22153.7°117.7°
N32C24C23C26159.5°140.9°
N32C24C23N3672.2°100.7°
C24N32C33H33149.3°154.7°
C24N32C33H33A26.0°34.6°
N32C24C25H2586.3°123.0°
N32C24C25H25A32.6°1.6°
N32C24C23H2339.2°22.5°
C25C24C23H24120.2°118.9°
C25C24N32S9120.7°65.2°
C25C24N32C3360.7°114.8°
C24C25N22H25120.0°119.4°
C24C25N22H25A121.2°119.3°
C24C25N22C2610.1°25.4°
C25C24C23C2631.2°21.9°
C25C24C23N36159.5°140.3°
C24C25H25H25A121.3°121.3°
C24C25N22HN22109.9°145.8°
C25C24C23H2389.1°96.5°
C23C24N32S9117.5°179.0°
C23C24N32C3361.1°0.9°
C23C24C25N2225.8°1.3°
C24C23C26N2225.8°37.4°
C24C23N36S10117.5°120.5°
C24C23C26N36127.9°118.4°
C24C23C26H23120.8°118.3°
C24C23N36H23119.4°123.2°
C24C23N36C3761.1°59.4°
C23C24C25H25145.8°118.0°
C23C24C25H25A95.3°120.6°
C24C23C26H2694.2°81.0°
C24C23C26H26A147.0°155.8°
C27C18C2H18180.0°179.9°
C18C27S9O40176.8°151.0°
C18C27S9N3261.0°95.4°
C18C27S9O1150.9°18.0°
C18C27C20H20179.7°180.0°
C27C18C2H2179.5°180.0°
S9C27C18C2179.9°180.0°
C27S9O40N32112.2°114.1°
C27S9O40O11121.9°123.0°
C27S9N32O11111.5°113.5°
C27S9N32C3387.4°82.8°
S9C27C20H200.5°0.0°
S9C27C18H180.1°0.1°
O40S9N32O11134.9°132.9°
O40S9N32C3326.2°30.8°
S9N32C33C3490.7°94.7°
S9N32C24H241.9°56.8°
S9N32C33H3329.3°25.3°
S9N32C33H33A152.6°145.3°
O11S9N32C33161.2°163.7°
N32C33C34H33120.0°120.0°
N32C33C34H33A116.7°120.0°
N32C33C34C35155.1°125.6°
C33N32C24H24179.5°123.1°
N32C33H33H33A117.0°120.0°
N32C33C34H3424.9°54.3°
C33C34C35H34180.0°179.9°
C33C34C35C111.2°180.0°
C34C33H33H33A117.1°120.0°
C34C35C10H100.9°60.0°
C34C35C10H10A120.8°180.0°
C34C35C10H10B119.2°60.1°
C35C34C33H3335.1°5.6°
C35C34C33H33A88.2°114.4°
C34C35C11H11175.2°90.0°
C34C35C11H11A64.7°30.0°
C34C35C11H11B55.3°150.1°
C11C35C10H10179.9°119.9°
C11C35C10H10A59.9°0.0°
C11C35C10H10B60.1°120.0°
C11C35C34H34178.8°0.1°
C35C11H11H11A120.0°120.0°
C35C11H11H11B120.0°119.9°
C35C11H11AH11B120.0°120.0°
C25N22C26HN22120.0°120.5°
C25N22C26C2310.1°39.2°
N22C25C24H2494.9°120.3°
N22C25H25H25A121.2°121.2°
C25N22C26H26109.9°79.2°
C25N22C26H26A131.3°157.7°
N22C26C23H26120.0°118.4°
N22C26C23H26A121.2°118.5°
N22C26C23N36153.7°155.8°
C26N22C25H25130.1°94.0°
C26N22C25H25A111.1°144.7°
N22C26C23H2394.9°81.0°
N22C26H26H26A121.3°123.1°
N2C9C4C3177.6°180.0°
N2C9O3C4173.8°180.0°
N2C9C4C72.7°0.0°
C9N2HN2HN2A180.0°179.9°
C4C3C19H3180.0°179.7°
C3C4C9O33.8°0.0°
C3C4C7C9179.7°180.0°
C3C4C7C211.9°0.0°
C4C3C19C280.5°0.0°
C3C4C7H7178.2°180.0°
C4C3C19H19179.5°180.0°
C19C3C4C71.4°0.0°
C19C3C4C9178.3°180.0°
C3C19C28S10179.9°180.0°
C3C19C28H19180.0°180.0°
C3C19C28C210.1°0.0°
O3C9C4C7176.5°179.9°
O3C9N2HN20.0°0.0°
O3C9N2HN2A180.0°179.9°
C4C7C21H7180.0°180.0°
C4C7C21C281.3°0.0°
C7C4C3H3178.6°179.7°
C4C7C21H21178.8°180.0°
C21C7C4C9177.8°180.0°
C7C21C28S10179.5°180.0°
C7C21C28C190.3°0.0°
C7C21C28H21180.0°180.0°
C4C9N2HN2173.7°180.0°
C4C9N2HN2A6.3°0.0°
C9C4C3H31.7°0.3°
C9C4C7H72.2°0.0°
O12S10C28N36111.9°113.5°
O12S10C28O41132.3°132.9°
O12S10N36O41134.9°132.9°
O12S10C28C1950.9°163.5°
O12S10C28C21129.3°16.5°
O12S10N36C2317.5°14.0°
O12S10N36C37161.2°166.0°
C28S10N36O41113.6°113.6°
S10C28C19C21179.8°180.0°
C28S10N36C2394.0°99.5°
C28S10N36C3787.3°80.4°
S10C28C19H190.1°0.0°
S10C28C21H210.5°0.1°
N36S10C28C1961.0°82.9°
N36S10C28C21118.8°97.1°
S10N36C23C26120.7°125.9°
S10N36C23C37178.6°179.9°
S10N36C37C3890.7°93.5°
S10N36C23H231.9°2.7°
S10N36C37H3729.3°146.5°
S10N36C37H37A152.6°26.6°
O41S10C28C19176.8°30.6°
O41S10C28C213.0°149.4°
O41S10N36C23152.5°146.9°
O41S10N36C3726.2°33.2°
C12C39C13C38179.1°180.0°
C12C39C38C37178.0°5.8°
C39C12H12H12A120.0°120.0°
C39C12H12H12B120.0°120.0°
C39C12H12AH12B120.0°120.0°
C12C39C13H135.6°93.4°
C12C39C13H13A125.6°146.7°
C12C39C13H13B114.4°26.6°
C12C39C38H382.0°174.3°
C13C39C38C371.2°174.3°
C13C39C12H12157.7°0.0°
C13C39C12H12A37.7°120.0°
C13C39C12H12B82.4°120.0°
C39C13H13H13A120.0°120.0°
C39C13H13H13B120.0°120.0°
C39C13H13AH13B120.0°120.0°
C13C39C38H38178.8°5.7°
C28C19C3H3179.5°179.7°
C19C28C21H21179.8°180.0°
C28C21C7H7178.7°180.0°
C21C28C19H19179.9°180.0°
C26C23N36H23118.8°123.2°
C26C23N36C3760.7°54.1°
C26C23C24H2489.0°97.0°
C23C26N22HN22130.1°159.7°
C23C26H26H26A121.2°123.1°
C23N36C37C3890.7°86.5°
N36C23C24H2439.3°21.4°
N36C23C26H2633.7°37.4°
N36C23C26H26A85.1°85.8°
C23N36C37H37149.3°33.5°
C23N36C37H37A26.0°153.5°
N36C37C38H37120.0°119.9°
N36C37C38H37A116.7°120.0°
N36C37C38C39155.1°126.8°
C37N36C23H23179.5°177.4°
N36C37H37H37A117.0°120.0°
N36C37C38H3824.9°53.3°
C37C38C39H38180.0°179.9°
C38C37H37H37A117.0°120.1°
C38C39C12H1223.1°180.0°
C38C39C12H12A143.1°60.0°
C38C39C12H12B96.8°60.0°
C38C39C13H13175.3°86.6°
C38C39C13H13A55.2°33.3°
C38C39C13H13B64.7°153.4°
C39C38C37H3735.1°6.9°
C39C38C37H37A88.2°113.2°
H5C5C20H201.3°0.3°
H10C10H10AH10B120.0°120.1°
H24C24C25H2525.1°1.0°
H24C24C25H25A143.9°120.4°
H24C24C23H23150.7°144.6°
H18C18C2H20.5°0.1°
H33C33C34H34144.9°174.3°
H33AC33C34H3491.8°65.6°
H11C11H11AH11B120.0°120.0°
H25C25N22HN2210.1°26.5°
H25AC25N22HN22128.9°94.8°
HN22N22C26H2610.1°41.3°
HN22N22C26H26A108.7°81.9°
H3C3C19H190.5°0.3°
H7C7C21H211.2°0.1°
H12C12H12AH12B120.0°120.0°
H13C13H13AH13B120.0°120.0°
H23C23C26H26145.1°160.6°
H23C23C26H26A26.3°37.5°
H37C37C38H38144.9°173.2°
H37AC37C38H3891.8°66.8°

224931

PDB entries from 2024-09-11

PDB statisticsPDBj update infoContact PDBjnumon