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Summary Geometry Related PDB entries

A1CUB

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	C2	sing	1.51Å	1.50Å
C2	O1	doub	1.21Å	1.22Å
C2	C3	sing	1.47Å	1.49Å
C3	C4	doub	1.40Å	1.39Å	Aromatic
C4	C5	sing	1.38Å	1.38Å	Aromatic
C5	C6	doub	1.38Å	1.39Å	Aromatic
C6	C7	sing	1.38Å	1.39Å	Aromatic
C7	C8	doub	1.38Å	1.38Å	Aromatic
C3	C8	sing	1.40Å	1.39Å	Aromatic
C6	S1	sing	1.76Å	1.77Å
S1	N1	sing	1.66Å	1.60Å
S1	O2	doub	1.42Å	1.43Å
S1	O3	doub	1.42Å	1.43Å
N1	H8	sing	0.97Å	1.00Å
N1	H9	sing	0.97Å	1.00Å
C4	H4	sing	1.08Å	1.08Å
C5	H5	sing	1.08Å	1.08Å
C7	H6	sing	1.08Å	1.08Å
C8	H7	sing	1.08Å	1.08Å
C1	H1	sing	1.09Å	1.10Å
C1	H2	sing	1.09Å	1.10Å
C1	H3	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	C2	O1	120.4°	120.0°
C1	C2	C3	119.3°	120.0°
C2	C1	H1	109.5°	109.5°
C2	C1	H2	109.4°	109.4°
C2	C1	H3	109.5°	109.5°
O1	C2	C3	120.3°	120.0°
C2	C3	C4	120.6°	120.2°
C2	C3	C8	120.6°	120.2°
C3	C4	C5	120.9°	119.8°
C4	C3	C8	118.8°	119.6°
C3	C4	H4	119.5°	120.1°
C4	C5	C6	119.4°	120.2°
C5	C4	H4	119.5°	120.1°
C4	C5	H5	120.3°	119.9°
C5	C6	C7	120.6°	120.4°
C5	C6	S1	119.6°	119.8°
C6	C5	H5	120.3°	119.9°
C6	C7	C8	119.4°	120.2°
C7	C6	S1	119.7°	119.8°
C6	C7	H6	120.3°	119.9°
C7	C8	C3	120.9°	119.8°
C8	C7	H6	120.3°	119.9°
C7	C8	H7	119.6°	120.1°
C3	C8	H7	119.6°	120.0°
C6	S1	N1	108.3°	107.2°
C6	S1	O2	107.3°	106.4°
C6	S1	O3	107.3°	106.4°
N1	S1	O2	107.1°	106.4°
N1	S1	O3	107.2°	106.4°
S1	N1	H8	109.5°	120.0°
S1	N1	H9	109.4°	120.0°
O2	S1	O3	119.1°	123.2°
H8	N1	H9	109.5°	120.0°
H1	C1	H2	109.5°	109.5°
H1	C1	H3	109.5°	109.5°
H2	C1	H3	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1	C2	O1	C3	179.8°	180.0°
C1	C2	C3	C4	172.9°	180.0°
C1	C2	C3	C8	6.8°	0.5°
C2	C1	H1	H2	120.0°	120.0°
C2	C1	H1	H3	120.0°	120.0°
C2	C1	H2	H3	120.0°	120.0°
O1	C2	C3	C4	6.9°	0.0°
O1	C2	C3	C8	173.4°	179.5°
O1	C2	C1	H1	0.0°	0.0°
O1	C2	C1	H2	120.0°	120.0°
O1	C2	C1	H3	120.0°	120.0°
C2	C3	C4	C8	179.7°	179.5°
C2	C3	C4	C5	179.8°	180.0°
C2	C3	C8	C7	179.8°	180.0°
C2	C3	C4	H4	0.1°	0.2°
C2	C3	C8	H7	0.2°	0.2°
C3	C2	C1	H1	179.7°	180.0°
C3	C2	C1	H2	59.7°	60.0°
C3	C2	C1	H3	60.3°	60.0°
C3	C4	C5	H4	180.0°	179.8°
C3	C4	C5	C6	0.2°	0.2°
C4	C3	C8	C7	0.1°	0.4°
C3	C4	C5	H5	179.8°	179.8°
C4	C3	C8	H7	179.9°	179.7°
C4	C5	C6	H5	180.0°	180.0°
C4	C5	C6	C7	0.2°	0.1°
C5	C4	C3	C8	0.1°	0.4°
C4	C5	C6	S1	179.9°	180.0°
C5	C6	C7	S1	179.7°	179.9°
C5	C6	C7	C8	0.2°	0.1°
C5	C6	S1	N1	96.8°	90.0°
C5	C6	S1	O2	147.9°	23.5°
C5	C6	S1	O3	18.7°	156.4°
C6	C5	C4	H4	179.8°	180.0°
C5	C6	C7	H6	179.8°	180.0°
C6	C7	C8	H6	180.0°	179.9°
C6	C7	C8	C3	0.1°	0.2°
C7	C6	S1	N1	82.9°	90.1°
C7	C6	S1	O2	32.5°	156.4°
C7	C6	S1	O3	161.6°	23.5°
C7	C6	C5	H5	179.8°	180.0°
C6	C7	C8	H7	179.8°	180.0°
C7	C8	C3	H7	180.0°	179.8°
C8	C7	C6	S1	179.9°	180.0°
C8	C3	C4	H4	179.8°	179.7°
C3	C8	C7	H6	179.8°	179.8°
C6	S1	N1	O2	115.5°	113.5°
C6	S1	N1	O3	115.6°	113.6°
C6	S1	O2	O3	122.1°	123.0°
C6	S1	N1	H8	180.0°	0.1°
C6	S1	N1	H9	60.0°	179.7°
S1	C6	C5	H5	0.1°	0.1°
S1	C6	C7	H6	0.1°	0.1°
N1	S1	O2	O3	121.8°	123.0°
S1	N1	H8	H9	120.0°	179.7°
O2	S1	N1	H8	64.5°	113.6°
O2	S1	N1	H9	175.5°	66.8°
O3	S1	N1	H8	64.5°	113.5°
O3	S1	N1	H9	55.5°	66.2°
H4	C4	C5	H5	0.2°	0.1°
H6	C7	C8	H7	0.2°	0.1°
H1	C1	H2	H3	120.0°	120.0°

250059

PDB entries from 2026-03-04

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