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Summary Geometry Related PDB entries

PXY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	C2	doub	1.38Å	1.32Å	Aromatic
C1	C6	sing	1.38Å	1.36Å	Aromatic
C1	C1'	sing	1.51Å	1.52Å
C2	C3	sing	1.38Å	1.38Å	Aromatic
C2	H2	sing	1.08Å	1.10Å
C3	C4	doub	1.38Å	1.36Å	Aromatic
C3	H3	sing	1.08Å	1.10Å
C4	C5	sing	1.38Å	1.35Å	Aromatic
C4	C4'	sing	1.51Å	1.53Å
C5	C6	doub	1.38Å	1.39Å	Aromatic
C5	H5	sing	1.08Å	1.10Å
C6	H6	sing	1.08Å	1.10Å
C1'	H1'1	sing	1.09Å	1.11Å
C1'	H1'2	sing	1.09Å	1.12Å
C1'	H1'3	sing	1.09Å	1.11Å
C4'	H4'1	sing	1.09Å	1.11Å
C4'	H4'2	sing	1.09Å	1.11Å
C4'	H4'3	sing	1.09Å	1.12Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C2	C1	C6	120.2°	120.0°
C2	C1	C1'	119.5°	120.0°
C1	C2	C3	120.6°	120.0°
C1	C2	H2	117.5°	120.0°
C6	C1	C1'	120.3°	120.0°
C1	C6	C5	120.1°	120.0°
C1	C6	H6	119.1°	120.0°
C1	C1'	H1'1	119.6°	109.4°
C1	C1'	H1'2	108.6°	109.5°
C1	C1'	H1'3	108.6°	109.5°
C3	C2	H2	121.9°	120.0°
C2	C3	C4	120.1°	120.0°
C2	C3	H3	120.4°	120.0°
C4	C3	H3	119.4°	120.0°
C3	C4	C5	119.6°	120.0°
C3	C4	C4'	119.8°	120.0°
C5	C4	C4'	120.7°	120.0°
C4	C5	C6	119.4°	120.0°
C4	C5	H5	119.1°	120.0°
C4	C4'	H4'1	119.8°	109.5°
C4	C4'	H4'2	108.5°	109.5°
C4	C4'	H4'3	108.5°	109.5°
C6	C5	H5	121.5°	120.0°
C5	C6	H6	120.8°	120.0°
H1'1	C1'	H1'2	108.6°	109.5°
H1'1	C1'	H1'3	108.6°	109.5°
H1'2	C1'	H1'3	101.4°	109.5°
H4'1	C4'	H4'2	108.5°	109.5°
H4'1	C4'	H4'3	108.5°	109.5°
H4'2	C4'	H4'3	101.4°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C2	C1	C6	C1'	178.9°	179.8°
C1	C2	C3	H2	180.0°	180.0°
C1	C2	C3	C4	1.9°	0.0°
C1	C2	C3	H3	178.2°	180.0°
C2	C1	C6	C5	1.1°	0.3°
C2	C1	C6	H6	178.9°	180.0°
C2	C1	C1'	H1'1	180.0°	90.0°
C2	C1	C1'	H1'2	54.7°	150.0°
C2	C1	C1'	H1'3	54.7°	30.0°
C6	C1	C2	C3	0.5°	0.2°
C6	C1	C2	H2	179.5°	179.8°
C1	C6	C5	C4	1.3°	0.2°
C1	C6	C5	H6	180.0°	179.8°
C1	C6	C5	H5	178.7°	179.8°
C6	C1	C1'	H1'1	1.1°	90.2°
C6	C1	C1'	H1'2	126.4°	29.8°
C6	C1	C1'	H1'3	124.2°	149.8°
C1'	C1	C2	C3	178.4°	180.0°
C1'	C1	C2	H2	1.6°	0.0°
C1'	C1	C6	C5	180.0°	179.9°
C1'	C1	C6	H6	0.0°	0.1°
C1	C1'	H1'1	H1'2	125.3°	120.0°
C1	C1'	H1'1	H1'3	125.3°	120.0°
C1	C1'	H1'2	H1'3	114.3°	120.0°
C2	C3	C4	H3	179.9°	179.9°
C2	C3	C4	C5	1.7°	0.0°
C2	C3	C4	C4'	178.9°	180.0°
H2	C2	C3	C4	178.1°	179.9°
H2	C2	C3	H3	1.9°	0.0°
C3	C4	C5	C4'	179.4°	180.0°
C3	C4	C5	C6	0.1°	0.1°
C3	C4	C5	H5	179.9°	179.9°
C3	C4	C4'	H4'1	180.0°	90.1°
C3	C4	C4'	H4'2	54.7°	149.9°
C3	C4	C4'	H4'3	54.7°	30.0°
H3	C3	C4	C5	178.4°	179.9°
H3	C3	C4	C4'	1.0°	0.1°
C4	C5	C6	H5	180.0°	180.0°
C4	C5	C6	H6	178.7°	180.0°
C5	C4	C4'	H4'1	0.6°	89.9°
C5	C4	C4'	H4'2	124.7°	30.1°
C5	C4	C4'	H4'3	125.8°	150.0°
C4'	C4	C5	C6	179.5°	179.9°
C4'	C4	C5	H5	0.5°	0.1°
C4	C4'	H4'1	H4'2	125.3°	120.0°
C4	C4'	H4'1	H4'3	125.3°	120.0°
C4	C4'	H4'2	H4'3	114.2°	120.0°
H5	C5	C6	H6	1.3°	0.0°
H1'1	C1'	H1'2	H1'3	114.2°	120.0°
H4'1	C4'	H4'2	H4'3	114.2°	120.0°

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PDB entries from 2024-09-11

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