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Summary Geometry Related PDB entries

SYR

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O3	C8	doub	1.22Å	1.20Å
C8	O4	sing	1.35Å	1.33Å
C8	C6	sing	1.47Å	1.48Å
O4	C10	sing	1.45Å	1.43Å
C10	H101	sing	1.09Å	1.11Å
C10	H102	sing	1.09Å	1.11Å
C10	H103	sing	1.09Å	1.11Å
C6	C5	doub	1.40Å	1.39Å	Aromatic
C6	C1	sing	1.40Å	1.39Å	Aromatic
C5	C4	sing	1.38Å	1.40Å	Aromatic
C5	H5	sing	1.08Å	1.10Å
C4	O2	sing	1.36Å	1.41Å
C4	C3	doub	1.39Å	1.40Å	Aromatic
O2	C7	sing	1.43Å	1.41Å
C7	H7C1	sing	1.09Å	1.12Å
C7	H7C2	sing	1.09Å	1.11Å
C7	H7C3	sing	1.09Å	1.12Å
C1	C2	doub	1.38Å	1.40Å	Aromatic
C1	H1	sing	1.08Å	1.10Å
C2	O5	sing	1.36Å	1.41Å
C2	C3	sing	1.39Å	1.40Å	Aromatic
O5	C9	sing	1.43Å	1.41Å
C9	H9C1	sing	1.09Å	1.12Å
C9	H9C2	sing	1.09Å	1.11Å
C9	H9C3	sing	1.09Å	1.11Å
C3	O1	sing	1.36Å	1.39Å
O1	HA	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O3	C8	O4	122.5°	120.0°
O3	C8	C6	123.0°	120.0°
O4	C8	C6	114.5°	120.0°
C8	O4	C10	118.0°	120.0°
C8	C6	C5	119.8°	120.0°
C8	C6	C1	121.5°	120.1°
O4	C10	H101	118.0°	109.5°
O4	C10	H102	109.1°	109.4°
O4	C10	H103	109.1°	109.5°
H101	C10	H102	109.1°	109.4°
H101	C10	H103	109.1°	109.5°
H102	C10	H103	101.0°	109.5°
C5	C6	C1	118.7°	119.9°
C6	C5	C4	121.5°	119.9°
C6	C5	H5	119.2°	120.1°
C6	C1	C2	121.3°	120.0°
C6	C1	H1	119.3°	120.0°
C4	C5	H5	119.2°	120.0°
C5	C4	O2	123.4°	119.9°
C5	C4	C3	118.8°	120.1°
O2	C4	C3	117.8°	120.0°
C4	O2	C7	116.1°	106.8°
C4	C3	C2	120.8°	120.2°
C4	C3	O1	119.8°	119.9°
O2	C7	H7C1	116.0°	109.5°
O2	C7	H7C2	109.8°	109.5°
O2	C7	H7C3	109.8°	109.5°
H7C1	C7	H7C2	109.8°	109.4°
H7C1	C7	H7C3	109.8°	109.5°
H7C2	C7	H7C3	100.4°	109.4°
C2	C1	H1	119.4°	120.0°
C1	C2	O5	123.5°	120.0°
C1	C2	C3	118.9°	120.0°
O5	C2	C3	117.6°	120.0°
C2	O5	C9	116.0°	106.8°
C2	C3	O1	119.4°	119.9°
O5	C9	H9C1	116.0°	109.4°
O5	C9	H9C2	109.9°	109.4°
O5	C9	H9C3	109.8°	109.5°
H9C1	C9	H9C2	109.9°	109.5°
H9C1	C9	H9C3	109.8°	109.4°
H9C2	C9	H9C3	100.3°	109.6°
C3	O1	HA	119.8°	106.8°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O3	C8	O4	C6	179.8°	179.9°
O3	C8	O4	C10	3.0°	0.1°
O3	C8	C6	C5	5.6°	0.1°
O3	C8	C6	C1	174.3°	179.7°
C8	O4	C10	H101	180.0°	180.0°
C8	O4	C10	H102	54.7°	60.1°
C8	O4	C10	H103	54.7°	59.9°
O4	C8	C6	C5	174.2°	180.0°
O4	C8	C6	C1	5.9°	0.2°
C6	C8	O4	C10	177.3°	180.0°
C8	C6	C5	C1	179.9°	179.8°
C8	C6	C5	C4	179.7°	180.0°
C8	C6	C5	H5	0.3°	0.0°
C8	C6	C1	C2	179.7°	179.7°
C8	C6	C1	H1	0.3°	0.2°
O4	C10	H101	H102	125.3°	119.9°
O4	C10	H101	H103	125.3°	120.1°
O4	C10	H102	H103	114.9°	120.0°
H101	C10	H102	H103	114.9°	120.0°
C6	C5	C4	H5	180.0°	180.0°
C6	C5	C4	O2	179.7°	180.0°
C6	C5	C4	C3	0.3°	0.0°
C5	C6	C1	C2	0.2°	0.4°
C5	C6	C1	H1	179.8°	180.0°
C1	C6	C5	C4	0.2°	0.2°
C1	C6	C5	H5	179.8°	179.8°
C6	C1	C2	H1	180.0°	179.6°
C6	C1	C2	O5	179.8°	179.8°
C6	C1	C2	C3	0.2°	0.4°
C5	C4	O2	C3	179.9°	180.0°
C5	C4	O2	C7	6.3°	0.0°
C5	C4	C3	C2	0.7°	0.0°
C5	C4	C3	O1	179.4°	179.9°
H5	C5	C4	O2	0.3°	0.0°
H5	C5	C4	C3	179.7°	180.0°
C4	O2	C7	H7C1	180.0°	180.0°
C4	O2	C7	H7C2	54.7°	60.0°
C4	O2	C7	H7C3	54.7°	60.0°
O2	C4	C3	C2	179.2°	180.0°
O2	C4	C3	O1	0.7°	0.1°
C3	C4	O2	C7	173.6°	180.0°
C4	C3	C2	C1	0.7°	0.2°
C4	C3	C2	O5	179.3°	180.0°
C4	C3	C2	O1	179.9°	180.0°
C4	C3	O1	HA	180.0°	90.0°
O2	C7	H7C1	H7C2	125.2°	120.0°
O2	C7	H7C1	H7C3	125.3°	120.0°
O2	C7	H7C2	H7C3	115.6°	120.0°
H7C1	C7	H7C2	H7C3	115.6°	120.0°
C1	C2	O5	C3	180.0°	179.8°
C1	C2	O5	C9	9.9°	0.2°
C1	C2	C3	O1	179.4°	179.8°
H1	C1	C2	O5	0.2°	0.2°
H1	C1	C2	C3	179.8°	180.0°
C2	O5	C9	H9C1	180.0°	180.0°
C2	O5	C9	H9C2	54.7°	60.0°
C2	O5	C9	H9C3	54.7°	60.0°
O5	C2	C3	O1	0.6°	0.1°
C3	C2	O5	C9	170.0°	180.0°
C2	C3	O1	HA	0.1°	90.0°
O5	C9	H9C1	H9C2	125.3°	120.0°
O5	C9	H9C1	H9C3	125.2°	119.9°
O5	C9	H9C2	H9C3	115.6°	120.0°
H9C1	C9	H9C2	H9C3	115.6°	120.0°

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PDB entries from 2026-03-18

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