Summary Geometry PCM/PTM Related PDB entries

YBT

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
Y1	O1	sing	2.23Å	2.39Å
Y1	O2	sing	2.26Å	2.37Å
Y1	O4	sing	2.33Å	2.37Å
Y1	O5	sing	2.23Å	2.37Å
Y1	N1	sing	2.34Å	2.68Å
O1	C2	sing	1.41Å	1.48Å
O1	HO1	sing	0.85Å	0.95Å
O2	C3	sing	1.44Å	1.45Å
O2	HO2	sing	0.84Å	0.95Å
O3	C4	sing	1.43Å	1.43Å
O3	HO3	sing	0.85Å	0.95Å
O4	C6	sing	1.42Å	1.47Å
O4	HO4	sing	0.84Å	0.95Å
O5	C8	sing	1.42Å	1.45Å
O5	HO5	sing	0.85Å	0.95Å
N1	C1	sing	1.53Å	1.58Å
N1	C5	sing	1.50Å	1.53Å
N1	C7	sing	1.50Å	1.53Å
C1	C2	sing	1.56Å	1.52Å
C1	C3	sing	1.56Å	1.57Å
C1	C4	sing	1.55Å	1.55Å
C2	H21	sing	0.99Å	1.10Å
C2	H22	sing	0.99Å	1.10Å
C3	H31	sing	0.99Å	1.10Å
C3	H32	sing	0.99Å	1.10Å
C4	H41	sing	0.99Å	1.10Å
C4	H42	sing	0.99Å	1.10Å
C5	C6	sing	1.52Å	1.50Å
C5	H51	sing	0.98Å	1.10Å
C5	H52	sing	0.98Å	1.10Å
C6	H61	sing	0.98Å	1.10Å
C6	H62	sing	0.98Å	1.10Å
C7	C8	sing	1.53Å	1.52Å
C7	H71	sing	0.98Å	1.10Å
C7	H72	sing	0.97Å	1.10Å
C8	H81	sing	0.98Å	1.10Å
C8	H82	sing	0.98Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	Y1	O2	70.7°	85.5°
O1	Y1	O4	132.0°	150.6°
O1	Y1	O5	83.2°	84.1°
O1	Y1	N1	66.3°	76.7°
Y1	O1	C2	122.7°	110.0°
Y1	O1	HO1	106.1°	120.9°
O2	Y1	O4	83.7°	92.7°
O2	Y1	O5	134.8°	161.9°
O2	Y1	N1	67.0°	80.4°
Y1	O2	C3	124.6°	107.7°
Y1	O2	HO2	105.6°	99.9°
O4	Y1	O5	87.6°	89.1°
O4	Y1	N1	66.4°	74.1°
Y1	O4	C6	119.8°	110.8°
Y1	O4	HO4	106.8°	111.5°
O5	Y1	N1	68.9°	82.8°
Y1	O5	C8	120.3°	106.4°
Y1	O5	HO5	106.7°	106.4°
Y1	N1	C1	100.9°	92.8°
Y1	N1	C5	111.7°	111.8°
Y1	N1	C7	106.0°	100.5°
C2	O1	HO1	106.1°	111.8°
O1	C2	C1	110.9°	112.4°
O1	C2	H21	109.1°	109.0°
O1	C2	H22	109.1°	108.1°
C3	O2	HO2	105.5°	109.3°
O2	C3	C1	109.1°	114.2°
O2	C3	H31	109.6°	108.0°
O2	C3	H32	109.6°	108.6°
C4	O3	HO3	109.5°	108.9°
O3	C4	C1	112.1°	113.9°
O3	C4	H41	108.8°	108.4°
O3	C4	H42	108.8°	108.2°
C6	O4	HO4	106.8°	109.9°
O4	C6	C5	110.2°	113.9°
O4	C6	H61	109.3°	108.7°
O4	C6	H62	109.3°	108.8°
C8	O5	HO5	106.7°	109.2°
O5	C8	C7	108.3°	114.3°
O5	C8	H81	109.7°	108.5°
O5	C8	H82	109.8°	108.8°
C1	N1	C5	115.8°	118.0°
C1	N1	C7	113.7°	118.5°
N1	C1	C2	110.7°	113.5°
N1	C1	C3	106.9°	112.6°
N1	C1	C4	116.6°	115.2°
C5	N1	C7	108.2°	111.8°
N1	C5	C6	113.6°	115.2°
N1	C5	H51	108.4°	109.6°
N1	C5	H52	108.4°	109.8°
N1	C7	C8	111.9°	115.3°
N1	C7	H71	108.9°	109.3°
N1	C7	H72	108.9°	110.0°
C2	C1	C3	106.5°	103.2°
C2	C1	C4	111.0°	105.7°
C1	C2	H21	109.1°	110.7°
C1	C2	H22	109.1°	109.6°
C3	C1	C4	104.4°	105.5°
C1	C3	H31	109.6°	108.9°
C1	C3	H32	109.6°	110.2°
C1	C4	H41	108.8°	109.6°
C1	C4	H42	108.8°	109.2°
H21	C2	H22	109.5°	107.0°
H31	C3	H32	109.5°	106.7°
H41	C4	H42	109.5°	107.2°
C6	C5	H51	108.4°	107.8°
C6	C5	H52	108.4°	107.5°
C5	C6	H61	109.3°	108.9°
C5	C6	H62	109.3°	108.9°
H51	C5	H52	109.5°	106.6°
H61	C6	H62	109.4°	107.4°
C8	C7	H71	108.9°	108.1°
C8	C7	H72	108.8°	107.5°
C7	C8	H81	109.8°	108.6°
C7	C8	H82	109.7°	109.1°
H71	C7	H72	109.5°	106.3°
H81	C8	H82	109.5°	107.3°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	Y1	O2	O4	138.7°	150.6°
O1	Y1	O2	O5	58.4°	55.1°
O1	Y1	O2	N1	71.7°	77.2°
O1	Y1	O4	O5	78.6°	76.3°
O1	Y1	O4	N1	10.6°	6.5°
O1	Y1	O5	N1	67.2°	77.2°
Y1	O1	C2	HO1	121.8°	137.2°
O1	Y1	O2	C3	56.5°	56.0°
O1	Y1	O2	HO2	65.6°	170.1°
O1	Y1	O4	C6	20.9°	37.5°
O1	Y1	O4	HO4	142.4°	85.2°
O1	Y1	O5	C8	84.1°	90.5°
O1	Y1	O5	HO5	154.4°	25.8°
O1	Y1	N1	C1	40.0°	46.4°
O1	Y1	N1	C5	163.7°	168.1°
O1	Y1	N1	C7	78.7°	73.2°
Y1	O1	C2	C1	2.0°	11.4°
Y1	O1	C2	H21	122.2°	111.7°
Y1	O1	C2	H22	118.2°	132.4°
O2	Y1	O4	O5	135.6°	162.0°
O2	Y1	O4	N1	67.6°	79.2°
O2	Y1	O5	N1	13.1°	22.0°
O2	Y1	O1	C2	47.5°	46.6°
O2	Y1	O1	HO1	169.3°	86.2°
Y1	O2	C3	HO2	122.0°	107.7°
O2	Y1	O4	C6	36.1°	48.2°
O2	Y1	O4	HO4	85.4°	170.9°
O2	Y1	O5	C8	30.0°	35.2°
O2	Y1	O5	HO5	151.5°	81.1°
O2	Y1	N1	C1	38.2°	41.2°
O2	Y1	N1	C5	85.5°	80.5°
O2	Y1	N1	C7	156.9°	160.8°
Y1	O2	C3	C1	12.9°	5.9°
Y1	O2	C3	H31	132.9°	115.4°
Y1	O2	C3	H32	107.0°	129.2°
O4	Y1	O5	N1	65.6°	74.1°
O4	Y1	O1	C2	14.5°	41.0°
O4	Y1	O1	HO1	107.4°	173.7°
O4	Y1	O2	C3	82.2°	94.6°
O4	Y1	O2	HO2	155.8°	19.5°
Y1	O4	C6	HO4	121.5°	123.6°
O4	Y1	O5	C8	48.6°	60.9°
O4	Y1	O5	HO5	72.8°	177.2°
O4	Y1	N1	C1	131.3°	136.8°
O4	Y1	N1	C5	7.7°	15.1°
O4	Y1	N1	C7	109.9°	103.6°
Y1	O4	C6	C5	51.3°	42.4°
Y1	O4	C6	H61	68.8°	163.9°
Y1	O4	C6	H62	171.4°	79.3°
O5	Y1	O1	C2	95.0°	118.6°
O5	Y1	O1	HO1	26.8°	108.7°
O5	Y1	O2	C3	2.0°	0.9°
O5	Y1	O2	HO2	124.0°	115.0°
O5	Y1	O4	C6	99.5°	113.8°
O5	Y1	O4	HO4	139.0°	8.9°
Y1	O5	C8	HO5	121.5°	114.4°
O5	Y1	N1	C1	131.8°	132.1°
O5	Y1	N1	C5	104.6°	106.2°
O5	Y1	N1	C7	13.1°	12.5°
Y1	O5	C8	C7	44.7°	38.1°
Y1	O5	C8	H81	75.1°	159.5°
Y1	O5	C8	H82	164.5°	84.1°
N1	Y1	O1	C2	25.1°	34.6°
N1	Y1	O1	HO1	96.7°	167.3°
N1	Y1	O2	C3	15.2°	21.2°
N1	Y1	O2	HO2	137.2°	92.9°
N1	Y1	O4	C6	31.5°	31.0°
N1	Y1	O4	HO4	153.0°	91.7°
N1	Y1	O5	C8	16.9°	13.2°
N1	Y1	O5	HO5	138.4°	103.1°
Y1	N1	C1	C5	120.7°	116.5°
Y1	N1	C1	C7	113.0°	103.5°
Y1	N1	C5	C7	116.3°	111.7°
Y1	N1	C1	C2	56.4°	57.8°
Y1	N1	C1	C3	59.1°	59.1°
Y1	N1	C1	C4	175.4°	179.9°
Y1	N1	C5	C6	14.1°	1.2°
Y1	N1	C5	H51	106.5°	123.0°
Y1	N1	C5	H52	134.7°	120.2°
Y1	N1	C7	C8	40.4°	36.9°
Y1	N1	C7	H71	80.0°	158.9°
Y1	N1	C7	H72	160.7°	84.9°
O1	C2	C1	N1	40.4°	36.2°
O1	C2	C1	H21	120.2°	122.1°
O1	C2	C1	H22	120.2°	120.1°
O1	C2	C1	C3	75.4°	86.1°
O1	C2	C1	C4	171.6°	163.4°
O1	C2	H21	H22	119.4°	116.6°
HO1	O1	C2	C1	119.8°	148.7°
HO1	O1	C2	H21	0.4°	25.6°
HO1	O1	C2	H22	120.0°	90.3°
O2	C3	C1	N1	51.0°	49.9°
O2	C3	C1	C2	67.3°	73.0°
O2	C3	C1	H31	120.0°	120.8°
O2	C3	C1	H32	119.9°	122.5°
O2	C3	C1	C4	175.2°	176.4°
O2	C3	H31	H32	120.2°	116.6°
HO2	O2	C3	C1	109.1°	113.5°
HO2	O2	C3	H31	10.8°	7.8°
HO2	O2	C3	H32	131.0°	123.1°
O3	C4	C1	N1	62.0°	54.0°
O3	C4	C1	C2	66.0°	72.2°
O3	C4	C1	C3	179.6°	178.8°
O3	C4	C1	H41	120.4°	121.7°
O3	C4	C1	H42	120.4°	121.1°
O3	C4	H41	H42	118.8°	116.6°
HO3	O3	C4	C1	180.0°	179.9°
HO3	O3	C4	H41	59.6°	57.8°
HO3	O3	C4	H42	59.6°	58.2°
O4	C6	C5	N1	39.2°	29.4°
O4	C6	C5	H61	120.1°	121.5°
O4	C6	C5	H62	120.1°	121.7°
O4	C6	C5	H51	81.4°	152.1°
O4	C6	C5	H52	159.9°	93.3°
O4	C6	H61	H62	119.7°	117.6°
HO4	O4	C6	C5	172.7°	81.2°
HO4	O4	C6	H61	52.6°	40.3°
HO4	O4	C6	H62	67.2°	157.1°
O5	C8	C7	N1	56.3°	56.0°
O5	C8	C7	H81	119.8°	121.3°
O5	C8	C7	H82	119.8°	122.1°
O5	C8	C7	H71	64.1°	178.6°
O5	C8	C7	H72	176.6°	67.1°
O5	C8	H81	H82	120.5°	117.4°
HO5	O5	C8	C7	166.2°	76.3°
HO5	O5	C8	H81	46.4°	45.1°
HO5	O5	C8	H82	74.0°	161.5°
C1	N1	C5	C7	129.0°	142.5°
N1	C1	C2	C3	115.8°	122.2°
N1	C1	C2	C4	131.2°	127.3°
N1	C1	C3	C4	124.2°	126.5°
N1	C1	C2	H21	79.8°	158.3°
N1	C1	C2	H22	160.6°	84.0°
N1	C1	C3	H31	171.0°	70.9°
N1	C1	C3	H32	68.9°	172.4°
N1	C1	C4	H41	58.4°	175.7°
N1	C1	C4	H42	177.6°	67.1°
C1	N1	C5	C6	100.6°	104.5°
C1	N1	C5	H51	138.8°	17.2°
C1	N1	C5	H52	20.0°	134.0°
C1	N1	C7	C8	150.3°	135.9°
C1	N1	C7	H71	29.9°	102.2°
C1	N1	C7	H72	89.4°	14.1°
C5	N1	C1	C2	177.2°	174.3°
C5	N1	C1	C3	61.6°	57.4°
C5	N1	C1	C4	54.6°	63.6°
N1	C5	C6	H51	120.6°	122.8°
N1	C5	C6	H52	120.6°	122.7°
N1	C5	H51	H52	118.1°	118.7°
N1	C5	C6	H61	80.9°	150.8°
N1	C5	C6	H62	159.4°	92.3°
C5	N1	C7	C8	79.6°	81.8°
C5	N1	C7	H71	160.1°	40.1°
C5	N1	C7	H72	40.8°	156.4°
C7	N1	C1	C2	56.6°	45.7°
C7	N1	C1	C3	172.1°	162.6°
C7	N1	C1	C4	71.6°	76.4°
C7	N1	C5	C6	130.5°	113.0°
C7	N1	C5	H51	9.9°	125.3°
C7	N1	C5	H52	109.0°	8.5°
N1	C7	C8	H71	120.4°	122.6°
N1	C7	C8	H72	120.4°	123.1°
N1	C7	H71	H72	118.9°	118.6°
N1	C7	C8	H81	63.5°	177.3°
N1	C7	C8	H82	176.1°	66.1°
C2	C1	C3	C4	117.5°	110.7°
C1	C2	H21	H22	119.3°	119.3°
C2	C1	C3	H31	52.7°	166.2°
C2	C1	C3	H32	172.8°	49.5°
C2	C1	C4	H41	173.6°	49.4°
C2	C1	C4	H42	54.3°	166.7°
C3	C1	C2	H21	164.4°	36.1°
C3	C1	C2	H22	44.8°	153.8°
C1	C3	H31	H32	120.2°	118.9°
C3	C1	C4	H41	59.2°	59.5°
C3	C1	C4	H42	60.0°	57.7°
C4	C1	C2	H21	51.4°	74.4°
C4	C1	C2	H22	68.2°	43.3°
C4	C1	C3	H31	64.9°	55.6°
C4	C1	C3	H32	55.3°	61.2°
C1	C4	H41	H42	118.8°	118.5°
C6	C5	H51	H52	118.1°	115.1°
C5	C6	H61	H62	119.6°	117.8°
H51	C5	C6	H61	158.5°	86.4°
H51	C5	C6	H62	38.8°	30.5°
H52	C5	C6	H61	39.7°	28.2°
H52	C5	C6	H62	80.0°	145.0°
C8	C7	H71	H72	118.8°	115.2°
C7	C8	H81	H82	120.5°	117.8°
H71	C7	C8	H81	176.1°	60.2°
H71	C7	C8	H82	55.7°	56.5°
H72	C7	C8	H81	56.8°	54.2°
H72	C7	C8	H82	63.5°	170.9°

Definition date:	2002-08-09
Last modified:	2026-09-01
Release status:	REL
Processing site:	RCSB