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Summary Geometry PCM/PTM Related PDB entries

AKK

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
CA	HA1	sing	1.09Å	1.10Å
CA	HA2	sing	1.09Å	1.10Å
CA	HA3	sing	1.09Å	1.10Å
CB	CA	sing	1.51Å	1.49Å
CC	CB	doub	1.32Å	1.35Å
ND	CC	sing	1.39Å	1.39Å
ND	HND1	sing	0.97Å	1.00Å
CB	HB1	sing	1.08Å	1.08Å
CC	HC1	sing	1.08Å	1.08Å
ND	HND2	sing	0.97Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
HA1	CA	HA2	109.4°	109.5°
HA1	CA	HA3	109.5°	109.5°
HA1	CA	CB	109.5°	109.4°
HA2	CA	HA3	109.5°	109.5°
HA2	CA	CB	109.5°	109.5°
HA3	CA	CB	109.5°	109.5°
CA	CB	CC	123.0°	120.0°
CA	CB	HB1	118.5°	120.1°
CB	CC	ND	128.7°	119.9°
CC	CB	HB1	118.5°	119.9°
CB	CC	HC1	115.7°	120.1°
CC	ND	HND1	109.5°	120.0°
ND	CC	HC1	115.7°	120.0°
CC	ND	HND2	109.5°	120.0°
HND1	ND	HND2	109.5°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
HA1	CA	HA2	HA3	120.0°	120.0°
HA1	CA	HA2	CB	120.0°	120.0°
HA1	CA	HA3	CB	120.1°	120.0°
HA1	CA	CB	CC	180.0°	180.0°
HA1	CA	CB	HB1	0.0°	0.0°
HA2	CA	HA3	CB	120.0°	120.0°
HA2	CA	CB	CC	60.0°	60.0°
HA2	CA	CB	HB1	120.0°	120.0°
HA3	CA	CB	CC	60.0°	60.0°
HA3	CA	CB	HB1	120.0°	120.0°
CA	CB	CC	HB1	180.0°	180.0°
CA	CB	CC	ND	0.8°	0.0°
CA	CB	CC	HC1	179.3°	180.0°
CB	CC	ND	HC1	180.0°	180.0°
CB	CC	ND	HND1	180.0°	180.0°
CB	CC	ND	HND2	60.0°	0.0°
CC	ND	HND1	HND2	120.0°	180.0°
ND	CC	CB	HB1	179.2°	180.0°
HND1	ND	CC	HC1	0.0°	0.0°
HB1	CB	CC	HC1	0.7°	0.0°
HC1	CC	ND	HND2	120.0°	180.0°

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PDB entries from 2026-03-25

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