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Summary Geometry Related PDB entries

YER

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O	C	sing	1.35Å	1.34Å
C	O1	doub	1.21Å	1.24Å
C1	C	sing	1.48Å	1.48Å
C1	C2	sing	1.40Å	1.39Å	Aromatic
C2	C3	doub	1.38Å	1.38Å	Aromatic
C3	C4	sing	1.38Å	1.38Å	Aromatic
C4	C5	doub	1.39Å	1.39Å	Aromatic
N	C5	sing	1.40Å	1.42Å
C6	N	sing	1.39Å	1.36Å
C6	N1	sing	1.32Å	1.34Å	Aromatic
N1	C7	doub	1.32Å	1.34Å	Aromatic
C7	C8	sing	1.39Å	1.38Å	Aromatic
C8	C9	doub	1.39Å	1.38Å	Aromatic
C9	N2	sing	1.32Å	1.34Å	Aromatic
N2	C6	doub	1.32Å	1.34Å	Aromatic
C5	C10	sing	1.39Å	1.39Å	Aromatic
C10	C1	doub	1.40Å	1.39Å	Aromatic
C4	H3	sing	1.08Å	1.08Å
C7	H5	sing	1.08Å	1.08Å
C8	H6	sing	1.08Å	1.08Å
C10	H8	sing	1.08Å	1.08Å
O	H	sing	0.97Å	0.95Å
C3	H2	sing	1.08Å	1.08Å
C2	H1	sing	1.08Å	1.08Å
N	H4	sing	0.97Å	1.00Å
C9	H7	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O	C	O1	123.7°	120.0°
O	C	C1	114.2°	120.0°
C	O	H	109.5°	117.1°
O1	C	C1	122.0°	120.0°
C	C1	C2	120.3°	120.1°
C	C1	C10	120.2°	120.1°
C1	C2	C3	120.4°	120.0°
C2	C1	C10	119.2°	119.8°
C1	C2	H1	119.7°	120.0°
C2	C3	C4	120.4°	120.2°
C2	C3	H2	119.8°	119.9°
C3	C2	H1	119.8°	120.0°
C3	C4	C5	119.8°	120.3°
C3	C4	H3	120.1°	119.9°
C4	C3	H2	119.8°	119.9°
C4	C5	N	121.5°	120.0°
C4	C5	C10	119.8°	120.0°
C5	C4	H3	120.1°	119.9°
C5	N	C6	132.3°	120.0°
N	C5	C10	118.6°	119.9°
C5	N	H4	113.8°	120.0°
N	C6	N1	117.1°	119.2°
N	C6	N2	115.9°	119.2°
C6	N	H4	113.8°	119.9°
C6	N1	C7	115.5°	120.7°
N1	C6	N2	126.4°	121.6°
N1	C7	C8	123.4°	119.2°
N1	C7	H5	118.3°	120.4°
C7	C8	C9	115.7°	118.6°
C8	C7	H5	118.3°	120.4°
C7	C8	H6	122.1°	120.7°
C8	C9	N2	123.5°	119.2°
C9	C8	H6	122.2°	120.7°
C8	C9	H7	118.3°	120.4°
C9	N2	C6	115.5°	120.7°
N2	C9	H7	118.3°	120.4°
C5	C10	C1	120.2°	119.8°
C5	C10	H8	119.9°	120.2°
C1	C10	H8	119.9°	120.1°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O	C	O1	C1	179.5°	180.0°
O	C	C1	C2	32.7°	0.1°
O	C	C1	C10	141.6°	180.0°
O1	C	C1	C2	147.8°	180.0°
O1	C	C1	C10	37.9°	0.0°
O1	C	O	H	0.0°	0.1°
C	C1	C2	C10	174.4°	180.0°
C	C1	C2	C3	172.4°	179.7°
C	C1	C10	C5	175.3°	180.0°
C	C1	C10	H8	4.7°	0.0°
C1	C	O	H	179.5°	180.0°
C	C1	C2	H1	7.6°	0.1°
C1	C2	C3	H1	180.0°	179.8°
C1	C2	C3	C4	2.0°	0.5°
C2	C1	C10	C5	0.9°	0.0°
C2	C1	C10	H8	179.1°	180.0°
C1	C2	C3	H2	178.0°	180.0°
C2	C3	C4	H2	180.0°	179.5°
C2	C3	C4	C5	0.9°	0.4°
C3	C2	C1	C10	2.0°	0.2°
C2	C3	C4	H3	179.1°	179.7°
C3	C4	C5	H3	180.0°	179.8°
C3	C4	C5	N	173.4°	179.8°
C3	C4	C5	C10	3.7°	0.2°
C4	C3	C2	H1	178.0°	179.7°
C4	C5	N	C10	177.2°	180.0°
C4	C5	N	C6	1.3°	146.5°
C4	C5	C10	C1	3.7°	0.0°
C4	C5	C10	H8	176.3°	180.0°
C5	C4	C3	H2	179.2°	180.0°
C4	C5	N	H4	178.7°	33.4°
C5	N	C6	H4	180.0°	179.9°
C5	N	C6	N1	11.5°	174.4°
C5	N	C6	N2	177.2°	5.5°
N	C5	C10	C1	173.5°	180.0°
N	C5	C4	H3	6.5°	0.0°
N	C5	C10	H8	6.5°	0.0°
N	C6	N1	N2	170.3°	180.0°
N	C6	N1	C7	167.8°	180.0°
N	C6	N2	C9	168.1°	180.0°
C6	N	C5	C10	175.9°	33.5°
C6	N1	C7	C8	0.8°	0.0°
N1	C6	N2	C9	2.3°	0.0°
C6	N1	C7	H5	179.2°	180.0°
N1	C6	N	H4	168.5°	5.6°
N1	C7	C8	H5	180.0°	180.0°
N1	C7	C8	C9	0.6°	0.0°
C7	N1	C6	N2	2.4°	0.0°
N1	C7	C8	H6	179.4°	179.9°
C7	C8	C9	H6	180.0°	179.9°
C7	C8	C9	N2	0.8°	0.1°
C7	C8	C9	H7	179.2°	180.0°
C8	C9	N2	H7	180.0°	180.0°
C8	C9	N2	C6	0.5°	0.1°
C9	C8	C7	H5	179.4°	179.9°
N2	C9	C8	H6	179.2°	180.0°
N2	C6	N	H4	2.8°	174.4°
C6	N2	C9	H7	179.5°	180.0°
C5	C10	C1	H8	180.0°	180.0°
C10	C5	C4	H3	176.3°	180.0°
C10	C5	N	H4	4.1°	146.6°
C10	C1	C2	H1	178.0°	180.0°
H3	C4	C3	H2	0.8°	0.2°
H5	C7	C8	H6	0.6°	0.0°
H6	C8	C9	H7	0.8°	0.1°
H2	C3	C2	H1	2.0°	0.2°

247536

PDB entries from 2026-01-14

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