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Summary Geometry Related PDB entries

YWF

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
CD	N	sing	1.47Å	1.65Å
CD	CB	sing	1.51Å	1.44Å
CB	CG	doub	1.33Å	1.22Å
O	C	doub	1.22Å	1.05Å
C	OXT	sing	1.35Å	1.59Å
N	H	sing	1.01Å	1.00Å
N	H2	sing	1.01Å	1.00Å
CD	HA2	sing	1.09Å	1.10Å
CD	HA1	sing	1.09Å	1.10Å
CB	HB2	sing	1.08Å	1.08Å
CG	HG2	sing	1.08Å	1.08Å
OXT	HXT	sing	0.97Å	0.95Å
CG	C	sing	1.47Å	1.53Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
N	CD	CB	85.3°	109.5°
CD	N	H	109.5°	111.0°
CD	N	H2	109.5°	111.0°
N	CD	HA2	115.1°	109.5°
N	CD	HA1	115.1°	109.5°
CD	CB	CG	149.2°	120.0°
CB	CD	HA2	115.1°	109.4°
CB	CD	HA1	115.1°	109.4°
CD	CB	HB2	105.4°	120.0°
CG	CB	HB2	105.4°	120.0°
CB	CG	HG2	98.7°	120.0°
CB	CG	C	162.7°	120.0°
O	C	OXT	113.8°	120.0°
O	C	CG	131.4°	120.0°
C	OXT	HXT	109.5°	117.0°
OXT	C	CG	110.0°	120.0°
H	N	H2	109.4°	111.0°
HA2	CD	HA1	109.5°	109.5°
HG2	CG	C	98.7°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N	CD	CB	HA2	115.6°	120.0°
N	CD	CB	HA1	115.6°	120.0°
N	CD	CB	CG	84.8°	125.0°
CD	N	H	H2	120.0°	124.0°
N	CD	HA2	HA1	131.5°	120.0°
N	CD	CB	HB2	95.2°	55.0°
CD	CB	CG	HB2	180.0°	180.0°
CB	CD	N	H	180.0°	180.0°
CB	CD	N	H2	60.0°	56.0°
CB	CD	HA2	HA1	131.6°	120.0°
CD	CB	CG	HG2	56.3°	0.0°
CD	CB	CG	C	123.7°	180.0°
CB	CG	C	O	50.2°	0.1°
CB	CG	C	OXT	156.3°	180.0°
CG	CB	CD	HA2	30.7°	5.0°
CG	CB	CD	HA1	159.6°	115.0°
CB	CG	HG2	C	180.0°	179.9°
O	C	OXT	CG	158.5°	179.9°
O	C	CG	HG2	129.8°	180.0°
O	C	OXT	HXT	0.0°	0.1°
OXT	C	CG	HG2	23.7°	0.1°
H	N	CD	HA2	64.4°	60.0°
H	N	CD	HA1	64.4°	60.0°
H2	N	CD	HA2	55.6°	64.0°
H2	N	CD	HA1	175.7°	176.0°
HA2	CD	CB	HB2	149.3°	175.0°
HA1	CD	CB	HB2	20.4°	65.0°
HB2	CB	CG	HG2	123.7°	180.0°
HB2	CB	CG	C	56.3°	0.1°
HXT	OXT	C	CG	158.6°	180.0°

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PDB entries from 2024-07-10

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