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Summary Geometry Related PDB entries

78Y

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C3	C2	sing	1.51Å	1.49Å
O	C	doub	1.22Å	1.22Å
C	C1	sing	1.48Å	1.43Å
C	N	sing	1.35Å	1.32Å
C2	C1	sing	1.41Å	1.42Å	Aromatic
C2	N3	doub	1.31Å	1.32Å	Aromatic
C1	N1	doub	1.32Å	1.34Å	Aromatic
N3	N2	sing	1.40Å	1.34Å	Aromatic
N1	N2	sing	1.29Å	1.33Å	Aromatic
N2	C4	sing	1.40Å	1.43Å
C4	C5	doub	1.39Å	1.39Å	Aromatic
C4	C9	sing	1.39Å	1.39Å	Aromatic
C5	C6	sing	1.38Å	1.39Å	Aromatic
C9	C8	doub	1.38Å	1.39Å	Aromatic
C6	C7	doub	1.38Å	1.38Å	Aromatic
C8	C7	sing	1.38Å	1.38Å	Aromatic
C5	H1	sing	1.08Å	1.08Å
C6	H2	sing	1.08Å	1.08Å
C7	H3	sing	1.08Å	1.08Å
C8	H4	sing	1.08Å	1.08Å
C9	H5	sing	1.08Å	1.08Å
N	H6	sing	0.97Å	1.00Å
N	H7	sing	0.97Å	1.00Å
C3	H8	sing	1.09Å	1.10Å
C3	H9	sing	1.09Å	1.10Å
C3	H10	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C3	C2	C1	129.0°	126.7°
C3	C2	N3	120.9°	126.7°
C2	C3	H8	109.5°	109.5°
C2	C3	H9	109.5°	109.5°
C2	C3	H10	109.5°	109.5°
O	C	C1	120.5°	120.0°
O	C	N	123.8°	120.0°
C1	C	N	115.7°	120.0°
C	C1	C2	129.2°	126.0°
C	C1	N1	123.7°	126.0°
C	N	H6	120.0°	120.0°
C	N	H7	120.0°	120.0°
C1	C2	N3	110.1°	106.6°
C2	C1	N1	107.1°	107.9°
C2	N3	N2	102.7°	107.2°
C1	N1	N2	104.3°	109.4°
N3	N2	N1	115.9°	108.8°
N3	N2	C4	122.2°	125.5°
N1	N2	C4	121.9°	125.6°
N2	C4	C5	119.8°	120.0°
N2	C4	C9	119.7°	120.1°
C5	C4	C9	120.3°	119.9°
C4	C5	C6	119.4°	119.9°
C4	C5	H1	120.3°	120.1°
C4	C9	C8	119.5°	119.9°
C4	C9	H5	120.3°	120.1°
C5	C6	C7	120.4°	120.1°
C6	C5	H1	120.3°	120.0°
C5	C6	H2	119.8°	119.9°
C9	C8	C7	120.4°	120.1°
C9	C8	H4	119.8°	119.9°
C8	C9	H5	120.2°	120.0°
C6	C7	C8	120.0°	120.1°
C7	C6	H2	119.8°	120.0°
C6	C7	H3	120.0°	120.0°
C8	C7	H3	120.0°	119.9°
C7	C8	H4	119.8°	120.0°
H6	N	H7	120.0°	120.0°
H8	C3	H9	109.5°	109.4°
H8	C3	H10	109.5°	109.4°
H9	C3	H10	109.4°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C3	C2	C1	C	1.3°	0.1°
C3	C2	C1	N3	178.8°	180.0°
C3	C2	C1	N1	179.3°	180.0°
C3	C2	N3	N2	179.2°	180.0°
C2	C3	H8	H9	120.0°	120.0°
C2	C3	H8	H10	120.0°	120.0°
C2	C3	H9	H10	120.0°	120.0°
O	C	C1	N	178.6°	179.9°
O	C	C1	C2	0.2°	0.1°
O	C	C1	N1	177.6°	180.0°
O	C	N	H6	0.0°	0.0°
O	C	N	H7	180.0°	180.0°
C	C1	C2	N1	178.0°	179.9°
C	C1	C2	N3	177.5°	179.9°
C	C1	N1	N2	177.7°	179.9°
C1	C	N	H6	178.6°	179.9°
C1	C	N	H7	1.5°	0.1°
N	C	C1	C2	178.8°	180.0°
N	C	C1	N1	1.1°	0.1°
C	N	H6	H7	180.0°	180.0°
C1	C2	N3	N2	0.3°	0.1°
C2	C1	N1	N2	0.5°	0.0°
C1	C2	C3	H8	178.7°	90.0°
C1	C2	C3	H9	61.3°	150.0°
C1	C2	C3	H10	58.7°	29.9°
N3	C2	C1	N1	0.5°	0.0°
C2	N3	N2	N1	0.1°	0.0°
C2	N3	N2	C4	177.3°	180.0°
N3	C2	C3	H8	0.0°	90.0°
N3	C2	C3	H9	120.0°	30.0°
N3	C2	C3	H10	120.0°	150.0°
C1	N1	N2	N3	0.4°	0.0°
C1	N1	N2	C4	177.6°	180.0°
N3	N2	N1	C4	177.2°	180.0°
N3	N2	C4	C5	3.6°	179.9°
N3	N2	C4	C9	171.4°	0.3°
N1	N2	C4	C5	179.3°	0.0°
N1	N2	C4	C9	5.6°	179.7°
N2	C4	C5	C9	175.0°	179.8°
N2	C4	C5	C6	174.1°	179.7°
N2	C4	C9	C8	173.6°	179.8°
N2	C4	C5	H1	5.9°	0.2°
N2	C4	C9	H5	6.4°	0.3°
C4	C5	C6	H1	180.0°	179.9°
C5	C4	C9	C8	1.4°	0.0°
C4	C5	C6	C7	0.1°	0.0°
C4	C5	C6	H2	179.9°	180.0°
C5	C4	C9	H5	178.6°	179.9°
C9	C4	C5	C6	0.9°	0.0°
C4	C9	C8	H5	180.0°	179.9°
C4	C9	C8	C7	0.8°	0.0°
C9	C4	C5	H1	179.0°	179.9°
C4	C9	C8	H4	179.2°	179.9°
C5	C6	C7	H2	180.0°	179.9°
C5	C6	C7	C8	0.7°	0.0°
C5	C6	C7	H3	179.3°	180.0°
C9	C8	C7	C6	0.3°	0.0°
C9	C8	C7	H4	180.0°	179.9°
C9	C8	C7	H3	179.7°	179.9°
C6	C7	C8	H3	180.0°	180.0°
C7	C6	C5	H1	179.9°	179.9°
C6	C7	C8	H4	179.7°	179.9°
C8	C7	C6	H2	179.2°	179.9°
C7	C8	C9	H5	179.2°	179.9°
H1	C5	C6	H2	0.1°	0.1°
H2	C6	C7	H3	0.7°	0.1°
H3	C7	C8	H4	0.2°	0.1°
H4	C8	C9	H5	0.8°	0.2°
H8	C3	H9	H10	120.0°	119.9°

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PDB entries from 2024-10-09

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