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Summary Geometry Related PDB entries

PYM

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	N1	sing	1.35Å	1.28Å
C1	O1	doub	1.21Å	1.29Å
C1	C2	sing	1.49Å	1.40Å
N1	HN12	sing	0.97Å	1.02Å
N1	HN11	sing	0.97Å	1.02Å
C2	O2	doub	1.21Å	1.23Å
C2	C3	sing	1.51Å	1.34Å
C3	H33	sing	1.09Å	1.11Å
C3	H32	sing	1.09Å	1.11Å
C3	H31	sing	1.09Å	1.12Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
N1	C1	O1	120.3°	120.0°
N1	C1	C2	118.6°	120.1°
C1	N1	HN12	118.6°	120.1°
C1	N1	HN11	120.3°	120.0°
O1	C1	C2	121.1°	120.0°
C1	C2	O2	126.1°	119.9°
C1	C2	C3	131.7°	120.0°
HN12	N1	HN11	121.1°	119.9°
O2	C2	C3	102.2°	120.0°
C2	C3	H33	131.7°	109.5°
C2	C3	H32	104.5°	109.5°
C2	C3	H31	104.5°	109.5°
H33	C3	H32	104.5°	109.4°
H33	C3	H31	104.5°	109.4°
H32	C3	H31	104.4°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N1	C1	O1	C2	179.7°	180.0°
C1	N1	HN12	HN11	179.8°	180.0°
N1	C1	C2	O2	0.3°	0.0°
N1	C1	C2	C3	179.9°	180.0°
O1	C1	N1	HN12	0.3°	0.0°
O1	C1	N1	HN11	180.0°	180.0°
O1	C1	C2	O2	180.0°	180.0°
O1	C1	C2	C3	0.3°	0.0°
C2	C1	N1	HN12	180.0°	180.0°
C2	C1	N1	HN11	0.2°	0.0°
C1	C2	O2	C3	179.7°	180.0°
C1	C2	C3	H33	180.0°	180.0°
C1	C2	C3	H32	54.7°	60.1°
C1	C2	C3	H31	54.7°	60.1°
O2	C2	C3	H33	0.4°	0.0°
O2	C2	C3	H32	125.0°	119.9°
O2	C2	C3	H31	125.6°	119.9°
C2	C3	H33	H32	125.3°	120.0°
C2	C3	H33	H31	125.3°	120.0°
C2	C3	H32	H31	109.5°	120.1°
H33	C3	H32	H31	109.5°	120.0°

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PDB entries from 2024-08-14

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