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

GDD

Bonds
First atomSecond atomBond order typeDistance
(experimental model)
Distance
(ideal model)
Properties
N2C2sing1.37Å1.37Å
N2H2N1sing0.97Å1.00Å
N2H2N2sing0.97Å1.00Å
C2N1sing1.36Å1.34Å
C2N3doub1.31Å1.37Å
N1C6sing1.35Å1.36Å
N1H1sing0.97Å1.00Å
N3C4sing1.34Å1.36Å
C4C5doub1.40Å1.46ÅAromatic
C4N9sing1.37Å1.34ÅAromatic
C5C6sing1.41Å1.46Å
C5N7sing1.36Å1.34ÅAromatic
C6O6doub1.22Å1.25Å
N7C8doub1.30Å1.34ÅAromatic
C8N9sing1.36Å1.34ÅAromatic
C8H8sing1.08Å1.08Å
N9C1'sing1.47Å1.46Å
C1'C2'sing1.54Å1.51Å
C1'O4'sing1.44Å1.44Å
C1'H1'sing1.09Å1.10Å
C2'O2'sing1.43Å1.41Å
C2'C3'sing1.55Å1.52Å
C2'H2'sing1.09Å1.10Å
O2'HAsing0.97Å0.95Å
C3'O3'sing1.43Å1.43Å
C3'C4'sing1.55Å1.53Å
C3'H3'sing1.09Å1.10Å
O3'HBsing0.97Å0.95Å
C4'O4'sing1.44Å1.45Å
C4'C5'sing1.53Å1.50Å
C4'H4'sing1.09Å1.10Å
C5'O5'sing1.43Å1.42Å
C5'H5'1sing1.09Å1.10Å
C5'H5'2sing1.09Å1.10Å
O5'PAsing1.61Å1.60Å
PAO1Adoub1.48Å1.48Å
PAO2Asing1.61Å1.52Å
PAO3Asing1.61Å1.64Å
O2AHO2Asing0.97Å0.95Å
O3APBsing1.61Å1.62Å
PBO2Bsing1.61Å1.51Å
PBO3Bdoub1.48Å1.50Å
PBO1Bsing1.61Å1.63Å
O2BHO2Bsing0.97Å0.95Å
O1BC11sing1.43Å1.43Å
C11O51sing1.43Å1.45Å
C11C21sing1.53Å1.55Å
C11H11sing1.09Å1.10Å
O51C51sing1.43Å1.44Å
C51C61sing1.53Å1.53Å
C51C41sing1.53Å1.55Å
C51H51sing1.09Å1.10Å
C61O6Asing1.43Å1.43Å
C61H611sing1.09Å1.10Å
C61H612sing1.09Å1.10Å
O6AH6Asing0.97Å0.95Å
C21O21sing1.43Å1.44Å
C21C31sing1.53Å1.52Å
C21H21sing1.09Å1.10Å
O21HCsing0.97Å0.95Å
C31O31sing1.43Å1.43Å
C31C41sing1.53Å1.55Å
C31H31sing1.09Å1.10Å
O31HDsing0.97Å0.95Å
C41O41sing1.43Å1.44Å
C41H41sing1.09Å1.10Å
O41HEsing0.97Å0.95Å
Angles
First atomSecond atomThird atomAngle
(experimental model)
Angle
(ideal model)
C2N2H2N1125.1°120.1°
C2N2H2N2109.8°120.0°
N2C2N1118.8°119.0°
N2C2N3119.5°119.0°
H2N1N2H2N2125.1°120.0°
N1C2N3121.7°121.9°
C2N1C6122.0°120.3°
C2N1H1119.0°119.9°
C2N3C4121.3°121.1°
C6N1H1119.0°119.8°
N1C6C5119.0°118.4°
N1C6O6123.4°120.8°
N3C4C5119.1°119.7°
N3C4N9136.7°134.2°
C5C4N9104.0°106.1°
C4C5C6116.8°118.6°
C4C5N7107.9°107.3°
C4N9C8110.5°107.5°
C4N9C1'126.7°126.2°
C6C5N7135.3°134.2°
C5C6O6117.6°120.8°
C5N7C8107.5°109.3°
N7C8N9110.0°109.8°
N7C8H8125.0°125.1°
N9C8H8125.0°125.1°
C8N9C1'122.7°126.3°
N9C1'C2'110.0°110.4°
N9C1'O4'111.8°110.4°
N9C1'H1'106.3°110.3°
C2'C1'O4'105.4°104.9°
C2'C1'H1'112.6°110.3°
C1'C2'O2'112.4°110.8°
C1'C2'C3'101.7°104.0°
C1'C2'H2'115.8°110.4°
O4'C1'H1'110.8°110.4°
C1'O4'C4'106.4°105.3°
O2'C2'C3'117.3°110.5°
O2'C2'H2'99.7°110.5°
C2'O2'HA109.5°106.9°
C3'C2'H2'110.7°110.5°
C2'C3'O3'112.3°110.6°
C2'C3'C4'101.2°104.1°
C2'C3'H3'112.2°110.6°
O3'C3'C4'106.8°110.5°
O3'C3'H3'107.1°110.5°
C3'O3'HB109.5°106.8°
C4'C3'H3'117.2°110.5°
C3'C4'O4'109.0°104.8°
C3'C4'C5'113.2°110.5°
C3'C4'H4'107.7°110.3°
O4'C4'C5'110.8°110.4°
O4'C4'H4'110.3°110.3°
C5'C4'H4'105.8°110.3°
C4'C5'O5'105.7°109.5°
C4'C5'H5'1111.6°109.5°
C4'C5'H5'2110.7°109.4°
O5'C5'H5'1111.6°109.5°
O5'C5'H5'2110.7°109.4°
C5'O5'PA122.6°106.8°
H5'1C5'H5'2106.6°109.5°
O5'PAO1A107.0°109.5°
O5'PAO2A111.5°109.5°
O5'PAO3A109.6°109.5°
O1APAO2A115.4°109.5°
O1APAO3A111.0°109.5°
O2APAO3A102.3°109.5°
PAO2AHO2A109.5°106.8°
PAO3APB136.7°106.8°
O3APBO2B112.7°109.5°
O3APBO3B111.3°109.5°
O3APBO1B102.8°109.5°
O2BPBO3B109.7°109.5°
O2BPBO1B112.5°109.5°
PBO2BHO2B109.5°106.8°
O3BPBO1B107.5°109.4°
PBO1BC11109.9°106.8°
O1BC11O51108.5°109.4°
O1BC11C21114.2°109.4°
O1BC11H11107.4°109.5°
O51C11C21110.9°109.8°
O51C11H11111.0°109.4°
C11O51C51116.0°107.6°
C21C11H11104.8°109.4°
C11C21O21110.8°109.6°
C11C21C31109.9°109.1°
C11C21H21107.4°109.5°
O51C51C61110.0°109.5°
O51C51C41110.8°109.8°
O51C51H51108.9°109.4°
C61C51C41111.3°109.4°
C61C51H51108.3°109.4°
C51C61O6A109.4°109.5°
C51C61H611109.5°109.5°
C51C61H612109.5°109.5°
C41C51H51107.5°109.4°
C51C41C31109.4°109.0°
C51C41O41109.4°109.5°
C51C41H41110.1°109.5°
O6AC61H611109.6°109.4°
O6AC61H612109.5°109.5°
C61O6AH6A109.5°106.8°
H611C61H612109.4°109.5°
O21C21C31106.6°109.5°
O21C21H21110.7°109.6°
C21O21HC109.5°106.8°
C31C21H21111.5°109.5°
C21C31O31110.5°109.8°
C21C31C41111.4°108.6°
C21C31H31108.4°109.6°
O31C31C41112.1°109.6°
O31C31H31107.7°109.6°
C31O31HD109.5°106.8°
C41C31H31106.6°109.6°
C31C41O41111.1°109.6°
C31C41H41108.4°109.6°
O41C41H41108.4°109.6°
C41O41HE109.5°106.8°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)
Torsion
(ideal model)
C2N2H2N1H2N2180.0°179.7°
N2C2N1N3177.8°179.7°
N2C2N1C6177.7°179.7°
N2C2N1H12.3°0.3°
N2C2N3C4179.6°180.0°
H2N1N2C2N1180.0°179.7°
H2N1N2C2N32.2°0.0°
H2N2N2C2N10.0°0.6°
H2N2N2C2N3177.8°179.7°
C2N1C6H1180.0°179.5°
N1C2N3C41.9°0.3°
C2N1C6C50.5°0.5°
C2N1C6O6178.6°179.7°
N3C2N1C60.0°0.6°
N3C2N1H1180.0°180.0°
C2N3C4C53.1°0.0°
C2N3C4N9177.9°180.0°
N1C6C5C40.8°0.3°
N1C6C5O6178.2°179.8°
N1C6C5N7179.7°179.7°
H1N1C6C5179.5°180.0°
H1N1C6O61.5°0.2°
N3C4C5N9176.3°180.0°
N3C4C5C62.5°0.0°
N3C4C5N7178.3°180.0°
N3C4N9C8178.5°180.0°
N3C4N9C1'4.4°0.0°
C4C5C6N7178.9°180.0°
C4C5C6O6177.4°180.0°
C4C5N7C80.0°0.0°
C5C4N9C83.2°0.0°
C5C4N9C1'179.8°180.0°
N9C4C5C6178.9°180.0°
N9C4C5N71.9°0.0°
C4N9C8N73.4°0.0°
C4N9C8C1'177.2°180.0°
C4N9C8H8176.6°180.0°
C4N9C1'C2'53.0°86.5°
C4N9C1'O4'63.7°157.9°
C4N9C1'H1'175.2°35.7°
C6C5N7C8179.0°180.0°
N7C5C6O61.5°0.0°
C5N7C8N92.0°0.0°
C5N7C8H8178.0°180.0°
N7C8N9H8180.0°180.0°
N7C8N9C1'179.4°180.0°
C8N9C1'C2'130.3°93.5°
C8N9C1'O4'112.9°22.0°
C8N9C1'H1'8.1°144.3°
H8C8N9C1'0.6°0.0°
N9C1'C2'O4'120.7°118.9°
N9C1'C2'H1'118.4°122.2°
N9C1'O4'H1'118.4°122.3°
N9C1'C2'O2'72.6°98.5°
N9C1'C2'C3'161.1°142.7°
N9C1'C2'H2'41.0°24.2°
N9C1'O4'C4'147.7°159.3°
C2'C1'O4'H1'122.1°118.9°
C1'C2'O2'C3'117.3°114.7°
C1'C2'O2'H2'123.2°122.7°
C1'C2'C3'H2'123.6°118.5°
C1'C2'O2'HA123.8°176.1°
C1'C2'C3'O3'78.1°118.8°
C1'C2'C3'C4'35.5°0.1°
C1'C2'C3'H3'161.2°118.5°
C2'C1'O4'C4'28.2°40.4°
O4'C1'C2'O2'166.8°142.6°
O4'C1'C2'C3'40.5°23.8°
O4'C1'C2'H2'79.6°94.7°
C1'O4'C4'C3'4.8°40.5°
C1'O4'C4'C5'130.0°159.5°
C1'O4'C4'H4'113.3°78.3°
H1'C1'C2'O2'45.8°23.7°
H1'C1'C2'C3'80.5°95.1°
H1'C1'C2'H2'159.4°146.4°
H1'C1'O4'C4'93.9°78.4°
O2'C2'C3'H2'113.4°122.5°
O2'C2'C3'O3'44.9°0.2°
O2'C2'C3'C4'158.4°118.8°
O2'C2'C3'H3'75.8°122.5°
C3'C2'O2'HA6.5°61.4°
C2'C3'O3'C4'110.1°114.7°
C2'C3'O3'H3'123.5°122.8°
C2'C3'C4'H3'122.3°118.7°
C2'C3'O3'HB19.8°65.4°
C2'C3'C4'O4'20.0°24.0°
C2'C3'C4'C5'103.8°143.0°
C2'C3'C4'H4'139.6°94.7°
H2'C2'O2'HA113.0°61.1°
H2'C2'C3'O3'158.3°122.7°
H2'C2'C3'C4'88.2°118.6°
H2'C2'C3'H3'37.6°0.0°
O3'C3'C4'H3'120.0°122.6°
O3'C3'C4'O4'97.7°142.7°
O3'C3'C4'C5'138.6°98.3°
O3'C3'C4'H4'21.9°24.0°
C4'C3'O3'HB90.3°180.0°
C3'C4'O4'C5'125.2°119.0°
C3'C4'O4'H4'118.0°118.8°
C3'C4'C5'H4'117.7°122.3°
C3'C4'C5'O5'44.4°178.1°
C3'C4'C5'H5'177.1°58.0°
C3'C4'C5'H5'2164.3°61.9°
H3'C3'O3'HB143.3°57.4°
H3'C3'C4'O4'142.3°94.7°
H3'C3'C4'C5'18.5°24.3°
H3'C3'C4'H4'98.1°146.5°
O4'C4'C5'H4'119.5°122.2°
O4'C4'C5'O5'78.4°66.4°
O4'C4'C5'H5'1160.2°173.6°
O4'C4'C5'H5'241.6°53.6°
C4'C5'O5'H5'1121.4°120.1°
C4'C5'O5'H5'2120.0°119.9°
C4'C5'H5'1H5'2121.0°120.0°
C4'C5'O5'PA178.9°180.0°
H4'C4'C5'O5'162.1°55.9°
H4'C4'C5'H5'140.7°64.2°
H4'C4'C5'H5'277.9°175.8°
O5'C5'H5'1H5'2121.0°120.0°
C5'O5'PAO1A39.9°55.0°
C5'O5'PAO2A166.9°65.0°
C5'O5'PAO3A80.5°175.0°
H5'1C5'O5'PA59.6°60.0°
H5'2C5'O5'PA58.9°60.0°
O5'PAO1AO2A124.7°120.0°
O5'PAO1AO3A119.5°120.0°
O5'PAO2AO3A117.0°120.0°
O5'PAO2AHO2A91.5°60.0°
O5'PAO3APB49.7°160.0°
O1APAO2AO3A120.6°120.0°
O1APAO2AHO2A146.1°180.0°
O1APAO3APB68.2°40.0°
O2APAO3APB168.0°80.0°
O3APAO2AHO2A25.5°60.0°
PAO3APBO2B45.0°75.0°
PAO3APBO3B78.8°45.0°
PAO3APBO1B166.4°164.9°
O3APBO2BO3B124.6°120.0°
O3APBO2BO1B115.7°120.0°
O3APBO3BO1B111.8°120.0°
O3APBO2BHO2B5.4°60.0°
O3APBO1BC1155.7°175.0°
O2BPBO3BO1B122.7°120.0°
O2BPBO1BC1165.8°65.0°
O3BPBO2BHO2B119.3°180.0°
O3BPBO1BC11173.2°55.0°
O1BPBO2BHO2B121.1°60.0°
PBO1BC11O51101.7°89.9°
PBO1BC11C21134.0°149.8°
PBO1BC11H1118.3°30.0°
O1BC11O51C21126.2°120.1°
O1BC11O51H11117.7°119.9°
O1BC11C21H11117.2°119.9°
O1BC11O51C5170.0°52.5°
O1BC11C21O21173.0°178.7°
O1BC11C21C3169.4°58.8°
O1BC11C21H2152.1°61.1°
O51C11C21H11119.8°120.0°
C11O51C51C61179.8°172.4°
C11O51C51C4156.7°67.6°
C11O51C51H5161.3°52.5°
O51C11C21O2164.0°58.6°
O51C11C21C3153.6°61.3°
O51C11C21H21175.0°178.8°
C21C11O51C5156.3°67.6°
C11C21O21C31119.6°119.6°
C11C21O21H21119.0°120.2°
C11C21C31H21119.0°119.8°
C11C21O21HC95.5°60.4°
C11C21C31O31179.8°173.6°
C11C21C31C4154.6°53.7°
C11C21C31H3162.4°66.0°
H11C11O51C51172.3°172.4°
H11C11C21O2155.8°61.4°
H11C11C21C31173.4°178.7°
H11C11C21H2165.2°58.8°
O51C51C61C41123.2°120.3°
O51C51C61H51118.9°119.9°
O51C51C41H51118.8°120.1°
O51C51C61O6A59.4°65.0°
O51C51C61H61160.6°175.0°
O51C51C61H612179.4°55.0°
O51C51C41C3153.7°61.2°
O51C51C41O41175.7°178.8°
O51C51C41H4165.3°58.7°
C61C51C41H51118.5°119.8°
C51C61O6AH611120.0°120.0°
C51C61O6AH612120.0°120.0°
C51C61H611H612120.0°120.0°
C51C61O6AH6A72.2°180.0°
C61C51C41C31176.4°178.7°
C61C51C41O4161.6°58.7°
C61C51C41H4157.4°61.5°
C41C51C61O6A177.4°174.7°
C41C51C61H61162.5°54.7°
C41C51C61H61257.4°65.3°
C51C41C31C2154.8°53.7°
C51C41C31O31179.1°173.6°
C51C41C31O41121.0°119.9°
C51C41C31H41120.1°119.8°
C51C41C31H3163.3°66.0°
C51C41O41H41120.0°120.1°
C51C41O41HE29.9°180.0°
H51C51C61O6A59.5°54.8°
H51C51C61H611179.5°65.1°
H51C51C61H61260.6°174.9°
H51C51C41C3165.1°58.8°
H51C51C41O4156.8°61.1°
H51C51C41H41175.8°178.7°
O6AC61H611H612120.1°120.0°
H611C61O6AH6A47.8°60.1°
H612C61O6AH6A167.8°59.9°
O21C21C31H21120.9°120.2°
O21C21C31O3159.7°53.6°
O21C21C31C4165.5°66.2°
O21C21C31H31177.5°174.1°
C31C21O21HC24.1°180.0°
C21C31O31C41124.8°119.2°
C21C31O31H31118.2°120.4°
C21C31C41H31118.1°119.7°
C21C31O31HD167.3°60.8°
C21C31C41O41175.8°173.6°
C21C31C41H4165.3°66.2°
H21C21O21HC145.5°59.8°
H21C21C31O3161.2°66.6°
H21C21C31C41173.6°173.6°
H21C21C31H3156.6°53.8°
O31C31C41H31117.6°120.4°
O31C31C41O4159.9°66.5°
O31C31C41H4159.1°53.8°
C41C31O31HD67.9°180.0°
C31C41O41H41119.0°120.2°
C31C41O41HE150.9°60.4°
H31C31O31HD49.1°59.6°
H31C31C41O4157.7°53.9°
H31C31C41H41176.7°174.1°
H41C41O41HE90.2°59.8°

222926

PDB entries from 2024-07-24

PDB statisticsPDBj update infoContact PDBjnumon