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Summary Geometry Related PDB entries

T5Y

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C	O	sing	1.36Å	1.35Å
C	C1	sing	1.39Å	1.41Å	Aromatic
C1	C2	doub	1.38Å	1.39Å	Aromatic
C2	C3	sing	1.39Å	1.41Å	Aromatic
C3	C4	doub	1.38Å	1.40Å	Aromatic
C4	N	sing	1.32Å	1.35Å	Aromatic
N	C	doub	1.32Å	1.37Å	Aromatic
C4	H4	sing	1.08Å	1.08Å
O	H	sing	0.97Å	0.95Å
C1	H1	sing	1.08Å	1.08Å
C2	H2	sing	1.08Å	1.08Å
C3	H3	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O	C	C1	117.8°	119.6°
O	C	N	117.6°	119.7°
C	O	H	109.5°	114.0°
C	C1	C2	116.8°	119.0°
C1	C	N	124.6°	120.6°
C	C1	H1	121.6°	120.5°
C1	C2	C3	120.2°	118.5°
C2	C1	H1	121.6°	120.5°
C1	C2	H2	119.9°	120.7°
C2	C3	C4	118.7°	119.3°
C3	C2	H2	119.9°	120.8°
C2	C3	H3	120.7°	120.4°
C3	C4	N	123.5°	120.8°
C3	C4	H4	118.2°	119.6°
C4	C3	H3	120.6°	120.3°
C4	N	C	116.2°	121.7°
N	C4	H4	118.2°	119.6°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O	C	C1	N	178.6°	180.0°
O	C	C1	C2	178.4°	180.0°
O	C	N	C4	178.2°	180.0°
O	C	C1	H1	1.6°	0.0°
C	C1	C2	H1	180.0°	179.9°
C	C1	C2	C3	0.2°	0.3°
C1	C	N	C4	0.4°	0.0°
C1	C	O	H	178.7°	90.0°
C	C1	C2	H2	179.8°	180.0°
C1	C2	C3	H2	180.0°	179.7°
C1	C2	C3	C4	0.3°	0.6°
C2	C1	C	N	0.2°	0.0°
C1	C2	C3	H3	179.7°	180.0°
C2	C3	C4	H3	180.0°	179.4°
C2	C3	C4	N	0.0°	0.6°
C2	C3	C4	H4	180.0°	179.7°
C3	C2	C1	H1	179.8°	179.7°
C3	C4	N	H4	180.0°	179.7°
C3	C4	N	C	0.3°	0.3°
C4	C3	C2	H2	179.7°	179.7°
N	C4	C3	H3	180.0°	180.0°
C	N	C4	H4	179.7°	180.0°
N	C	O	H	0.0°	90.0°
N	C	C1	H1	179.9°	180.0°
H4	C4	C3	H3	0.0°	0.3°
H1	C1	C2	H2	0.2°	0.0°
H2	C2	C3	H3	0.2°	0.3°

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PDB entries from 2024-05-15

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