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Summary Geometry Related PDB entries

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Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C01	O02	sing	1.43Å	1.39Å
O14	C12	doub	1.21Å	1.20Å
N11	C05	sing	1.35Å	1.37Å	Aromatic
N11	C10	doub	1.31Å	1.30Å	Aromatic
C04	C05	doub	1.40Å	1.39Å	Aromatic
C04	C03	sing	1.38Å	1.38Å	Aromatic
C05	C06	sing	1.41Å	1.36Å	Aromatic
O02	C03	sing	1.36Å	1.37Å
C12	C10	sing	1.48Å	1.49Å
C12	O13	sing	1.35Å	1.23Å
C10	O09	sing	1.35Å	1.27Å	Aromatic
C03	C08	doub	1.39Å	1.37Å	Aromatic
C06	O09	sing	1.35Å	1.30Å	Aromatic
C06	C07	doub	1.39Å	1.39Å	Aromatic
C08	C07	sing	1.38Å	1.37Å	Aromatic
C01	H1	sing	1.09Å	1.10Å
C01	H2	sing	1.09Å	1.10Å
C01	H3	sing	1.09Å	1.10Å
C04	H4	sing	1.08Å	1.08Å
C07	H5	sing	1.08Å	1.08Å
C08	H6	sing	1.08Å	1.08Å
O13	H7	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C01	O02	C03	112.5°	117.0°
O02	C01	H1	109.5°	109.5°
O02	C01	H2	109.5°	109.5°
O02	C01	H3	109.4°	109.5°
O14	C12	C10	115.9°	120.0°
O14	C12	O13	120.5°	120.0°
C05	N11	C10	106.1°	109.0°
N11	C05	C04	136.3°	133.6°
N11	C05	C06	105.9°	106.8°
N11	C10	C12	127.2°	125.0°
N11	C10	O09	110.7°	110.1°
C05	C04	C03	120.8°	119.7°
C04	C05	C06	117.8°	119.6°
C05	C04	H4	119.6°	120.1°
C04	C03	O02	121.0°	119.8°
C04	C03	C08	120.8°	120.4°
C03	C04	H4	119.6°	120.2°
C05	C06	O09	106.8°	106.3°
C05	C06	C07	121.6°	119.9°
O02	C03	C08	118.2°	119.8°
C10	C12	O13	123.5°	120.0°
C12	C10	O09	122.0°	125.0°
C12	O13	H7	109.5°	117.0°
C10	O09	C06	110.5°	107.9°
C03	C08	C07	118.6°	120.5°
C03	C08	H6	120.7°	119.8°
O09	C06	C07	131.6°	133.9°
C06	C07	C08	120.5°	120.0°
C06	C07	H5	119.7°	120.0°
C08	C07	H5	119.8°	120.0°
C07	C08	H6	120.7°	119.8°
H1	C01	H2	109.5°	109.5°
H1	C01	H3	109.5°	109.4°
H2	C01	H3	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C01	O02	C03	C04	13.4°	180.0°
C01	O02	C03	C08	166.1°	0.1°
O02	C01	H1	H2	120.0°	120.0°
O02	C01	H1	H3	120.0°	120.0°
O02	C01	H2	H3	120.0°	120.1°
O14	C12	C10	N11	2.9°	0.3°
O14	C12	C10	O13	177.8°	180.0°
O14	C12	C10	O09	176.8°	180.0°
O14	C12	O13	H7	0.0°	0.0°
N11	C05	C04	C06	179.6°	179.5°
N11	C05	C04	C03	179.8°	179.5°
C05	N11	C10	C12	179.3°	179.7°
C05	N11	C10	O09	0.4°	0.1°
N11	C05	C06	O09	0.5°	0.4°
N11	C05	C06	C07	179.8°	179.7°
N11	C05	C04	H4	0.2°	0.5°
C10	N11	C05	C04	179.1°	179.8°
C10	N11	C05	C06	0.6°	0.2°
N11	C10	C12	O09	179.7°	179.6°
N11	C10	C12	O13	179.3°	179.7°
N11	C10	O09	C06	0.1°	0.3°
C05	C04	C03	H4	180.0°	180.0°
C05	C04	C03	O02	180.0°	180.0°
C05	C04	C03	C08	0.5°	0.0°
C04	C05	C06	O09	179.2°	180.0°
C04	C05	C06	C07	0.5°	0.0°
C03	C04	C05	C06	0.6°	0.0°
C04	C03	O02	C08	179.6°	180.0°
C04	C03	C08	C07	0.2°	0.0°
C04	C03	C08	H6	179.8°	180.0°
C05	C06	O09	C10	0.3°	0.4°
C05	C06	O09	C07	179.6°	179.9°
C05	C06	C07	C08	0.2°	0.0°
C06	C05	C04	H4	179.4°	180.0°
C05	C06	C07	H5	179.8°	180.0°
O02	C03	C08	C07	179.8°	180.0°
C03	O02	C01	H1	180.0°	60.1°
C03	O02	C01	H2	60.0°	59.9°
C03	O02	C01	H3	60.0°	180.0°
O02	C03	C04	H4	0.0°	0.0°
O02	C03	C08	H6	0.2°	0.0°
C12	C10	O09	C06	179.7°	180.0°
C10	C12	O13	H7	177.7°	180.0°
O13	C12	C10	O09	1.0°	0.1°
C10	O09	C06	C07	179.9°	179.7°
C03	C08	C07	C06	0.0°	0.0°
C03	C08	C07	H6	180.0°	180.0°
C08	C03	C04	H4	179.5°	180.0°
C03	C08	C07	H5	179.9°	180.0°
O09	C06	C07	C08	179.4°	179.9°
O09	C06	C07	H5	0.6°	0.1°
C06	C07	C08	H5	180.0°	180.0°
C06	C07	C08	H6	179.9°	180.0°
H1	C01	H2	H3	120.0°	120.0°
H5	C07	C08	H6	0.1°	0.0°

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PDB entries from 2026-02-04

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