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Summary Geometry Related PDB entries

GPJ

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
P1	O1	doub	1.48Å	1.47Å
P1	O2	sing	1.61Å	1.46Å
P1	O3	sing	1.61Å	1.52Å
P1	C1	sing	1.82Å	1.75Å
O2	HO2	sing	0.97Å	0.95Å
O3	HO3	sing	0.97Å	0.95Å
O4	C3	sing	1.34Å	1.28Å
O4	HO4	sing	0.97Å	0.95Å
O5	C3	doub	1.21Å	1.22Å
C1	N1	sing	1.47Å	1.45Å
C1	H11	sing	1.09Å	1.12Å
C1	H12	sing	1.09Å	1.12Å
C2	C3	sing	1.51Å	1.52Å
C2	N1	sing	1.47Å	1.50Å
C2	H21	sing	1.09Å	1.12Å
C2	H22	sing	1.09Å	1.12Å
N1	HN	sing	1.01Å	1.02Å
N1	HN11	sing	1.01Å	1.02Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	P1	O2	114.5°	109.5°
O1	P1	O3	112.1°	109.5°
O1	P1	C1	108.6°	109.5°
O2	P1	O3	111.4°	109.4°
O2	P1	C1	101.2°	109.4°
P1	O2	HO2	114.5°	106.9°
O3	P1	C1	108.4°	109.5°
P1	O3	HO3	112.0°	106.8°
P1	C1	N1	109.7°	109.5°
P1	C1	H11	112.1°	109.5°
P1	C1	H12	112.1°	109.4°
C3	O4	HO4	125.7°	120.0°
O4	C3	O5	125.7°	120.0°
O4	C3	C2	118.9°	120.0°
O5	C3	C2	115.4°	120.0°
N1	C1	H11	112.1°	109.5°
N1	C1	H12	112.2°	109.5°
C1	N1	C2	118.8°	109.4°
C1	N1	HN	108.8°	109.5°
C1	N1	HN11	108.9°	109.5°
H11	C1	H12	98.2°	109.5°
C3	C2	N1	109.9°	109.4°
C3	C2	H21	112.1°	109.4°
C3	C2	H22	112.1°	109.5°
N1	C2	H21	112.1°	109.4°
N1	C2	H22	112.1°	109.5°
C2	N1	HN	108.9°	109.5°
C2	N1	HN11	108.9°	109.5°
H21	C2	H22	98.3°	109.5°
HN	N1	HN11	101.2°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	P1	O2	O3	128.5°	120.0°
O1	P1	O2	C1	116.6°	120.0°
O1	P1	O3	C1	119.8°	120.0°
O1	P1	O2	HO2	180.0°	180.0°
O1	P1	O3	HO3	180.0°	60.0°
O1	P1	C1	N1	29.9°	55.0°
O1	P1	C1	H11	95.4°	175.0°
O1	P1	C1	H12	155.2°	65.0°
O2	P1	O3	C1	110.5°	120.0°
O2	P1	O3	HO3	50.2°	60.0°
O2	P1	C1	N1	150.7°	65.0°
O2	P1	C1	H11	25.4°	55.0°
O2	P1	C1	H12	84.0°	175.0°
O3	P1	O2	HO2	51.5°	60.0°
O3	P1	C1	N1	92.1°	175.0°
O3	P1	C1	H11	142.6°	65.0°
O3	P1	C1	H12	33.2°	55.1°
C1	P1	O2	HO2	63.4°	60.0°
C1	P1	O3	HO3	60.2°	179.9°
P1	C1	N1	H11	125.3°	120.0°
P1	C1	N1	H12	125.3°	119.9°
P1	C1	H11	H12	118.0°	120.0°
P1	C1	N1	C2	176.0°	179.9°
P1	C1	N1	HN	58.7°	60.0°
P1	C1	N1	HN11	50.8°	60.0°
O4	C3	O5	C2	179.1°	179.9°
O4	C3	C2	N1	5.3°	180.0°
O4	C3	C2	H21	130.6°	60.1°
O4	C3	C2	H22	120.0°	60.0°
HO4	O4	C3	O5	180.0°	0.0°
HO4	O4	C3	C2	0.9°	179.9°
O5	C3	C2	N1	175.5°	0.1°
O5	C3	C2	H21	50.2°	120.0°
O5	C3	C2	H22	59.2°	120.0°
N1	C1	H11	H12	118.1°	120.0°
C1	N1	C2	C3	178.3°	180.0°
C1	N1	C2	HN	125.2°	120.0°
C1	N1	C2	HN11	125.2°	119.9°
C1	N1	C2	H21	56.4°	60.1°
C1	N1	C2	H22	53.0°	60.0°
C1	N1	HN	HN11	114.6°	120.0°
H11	C1	N1	C2	50.8°	60.1°
H11	C1	N1	HN	176.0°	60.0°
H11	C1	N1	HN11	74.5°	180.0°
H12	C1	N1	C2	58.7°	60.0°
H12	C1	N1	HN	66.5°	179.9°
H12	C1	N1	HN11	176.1°	59.9°
C3	C2	N1	H21	125.3°	119.9°
C3	C2	N1	H22	125.3°	120.0°
C3	C2	H21	H22	118.0°	120.0°
C3	C2	N1	HN	56.5°	59.9°
C3	C2	N1	HN11	53.0°	60.1°
N1	C2	H21	H22	117.9°	120.1°
C2	N1	HN	HN11	114.6°	120.0°
H21	C2	N1	HN	68.8°	60.0°
H21	C2	N1	HN11	178.3°	180.0°
H22	C2	N1	HN	178.2°	179.9°
H22	C2	N1	HN11	72.3°	59.9°

223166

PDB entries from 2024-07-31

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