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Summary Geometry Related PDB entries

Y3P

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O3	C2	sing	1.35Å	1.39Å
O4	C4	doub	1.22Å	1.27Å
C2	C1	sing	1.48Å	1.55Å
C2	C3	doub	1.35Å	1.32Å
C4	C3	sing	1.47Å	1.50Å
C4	O5	sing	1.35Å	1.27Å
O2	C1	doub	1.21Å	1.31Å
C1	O1	sing	1.35Å	1.24Å
O1	H1	sing	0.97Å	0.95Å
C3	HC3	sing	1.08Å	1.08Å
O3	HO3	sing	0.97Å	0.95Å
O5	H2	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O3	C2	C1	115.4°	120.0°
O3	C2	C3	121.9°	120.0°
C2	O3	HO3	109.5°	114.0°
O4	C4	C3	116.1°	120.0°
O4	C4	O5	124.2°	120.0°
C1	C2	C3	122.6°	120.0°
C2	C1	O2	117.3°	120.0°
C2	C1	O1	116.7°	120.0°
C2	C3	C4	122.4°	120.0°
C2	C3	HC3	118.8°	120.0°
C3	C4	O5	119.6°	120.0°
C4	C3	HC3	118.8°	120.0°
C4	O5	H2	109.5°	117.0°
O2	C1	O1	126.0°	120.0°
C1	O1	H1	109.5°	116.9°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O3	C2	C1	C3	176.5°	180.0°
O3	C2	C3	C4	0.1°	5.3°
O3	C2	C1	O2	111.2°	179.8°
O3	C2	C1	O1	71.6°	0.0°
O3	C2	C3	HC3	179.9°	174.6°
O4	C4	C3	C2	3.1°	5.9°
O4	C4	C3	O5	177.3°	180.0°
O4	C4	C3	HC3	176.9°	174.1°
O4	C4	O5	H2	0.0°	0.0°
C1	C2	C3	C4	176.3°	174.6°
C2	C1	O2	O1	176.9°	179.8°
C2	C1	O1	H1	176.9°	180.0°
C1	C2	C3	HC3	3.7°	5.4°
C1	C2	O3	HO3	175.2°	174.3°
C2	C3	C4	HC3	180.0°	180.0°
C2	C3	C4	O5	179.6°	174.2°
C3	C2	C1	O2	72.3°	0.3°
C3	C2	C1	O1	104.9°	180.0°
C3	C2	O3	HO3	1.4°	5.6°
C3	C4	O5	H2	177.1°	180.0°
O5	C4	C3	HC3	0.4°	5.9°
O2	C1	O1	H1	0.0°	0.2°

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PDB entries from 2024-08-14

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