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Summary Geometry Related PDB entries

MP5

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	C2	doub	1.40Å	1.42Å	Aromatic
C1	C3	sing	1.51Å	1.46Å
C1	C6	sing	1.38Å	1.41Å	Aromatic
C2	N1	sing	1.39Å	1.37Å
C2	N2	sing	1.33Å	1.40Å	Aromatic
C3	O1	sing	1.43Å	1.37Å
C3	H31	sing	1.09Å	1.12Å
C3	H32	sing	1.09Å	1.12Å
N1	HN11	sing	0.97Å	1.02Å
N1	HN12	sing	0.97Å	1.02Å
N2	C4	doub	1.32Å	1.36Å	Aromatic
C4	C5	sing	1.51Å	1.53Å
C4	N3	sing	1.32Å	1.41Å	Aromatic
C5	H51	sing	1.09Å	1.11Å
C5	H52	sing	1.09Å	1.11Å
C5	H53	sing	1.09Å	1.12Å
N3	C6	doub	1.33Å	1.39Å	Aromatic
C6	H6	sing	1.08Å	1.10Å
O1	P1	sing	1.61Å	1.61Å
P1	O2	sing	1.61Å	1.59Å
P1	O3	doub	1.48Å	1.62Å
P1	O4	sing	1.61Å	1.41Å
O2	HO2	sing	0.97Å	0.95Å
O4	HO4	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C2	C1	C3	121.0°	120.8°
C2	C1	C6	117.3°	118.3°
C1	C2	N1	121.1°	120.5°
C1	C2	N2	120.4°	119.0°
C3	C1	C6	121.8°	120.9°
C1	C3	O1	113.3°	109.5°
C1	C3	H31	110.8°	109.5°
C1	C3	H32	110.8°	109.5°
C1	C6	N3	123.4°	119.2°
C1	C6	H6	119.0°	120.4°
N1	C2	N2	118.4°	120.5°
C2	N1	HN11	108.1°	120.0°
C2	N1	HN12	121.1°	120.0°
C2	N2	C4	119.5°	120.7°
O1	C3	H31	110.8°	109.4°
O1	C3	H32	110.8°	109.5°
C3	O1	P1	118.6°	106.8°
H31	C3	H32	99.5°	109.4°
HN11	N1	HN12	108.1°	120.0°
N2	C4	C5	117.7°	119.1°
N2	C4	N3	123.1°	121.9°
C5	C4	N3	119.1°	119.1°
C4	C5	H51	109.3°	109.5°
C4	C5	H52	117.7°	109.5°
C4	C5	H53	109.2°	109.4°
C4	N3	C6	116.1°	121.0°
H51	C5	H52	109.2°	109.5°
H51	C5	H53	100.9°	109.4°
H52	C5	H53	109.2°	109.5°
N3	C6	H6	117.6°	120.4°
O1	P1	O2	93.2°	109.5°
O1	P1	O3	113.4°	109.5°
O1	P1	O4	114.1°	109.5°
O2	P1	O3	100.3°	109.4°
O2	P1	O4	117.9°	109.5°
P1	O2	HO2	93.2°	106.8°
O3	P1	O4	115.3°	109.5°
P1	O4	HO4	114.1°	106.7°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C2	C1	C3	C6	178.9°	180.0°
C1	C2	N1	N2	179.6°	179.7°
C2	C1	C3	O1	86.5°	180.0°
C2	C1	C3	H31	38.7°	60.0°
C2	C1	C3	H32	148.2°	60.0°
C1	C2	N1	HN11	54.7°	180.0°
C1	C2	N1	HN12	180.0°	0.0°
C1	C2	N2	C4	0.7°	0.6°
C2	C1	C6	N3	1.8°	0.0°
C2	C1	C6	H6	178.2°	180.0°
C3	C1	C2	N1	3.7°	0.0°
C3	C1	C2	N2	175.9°	179.7°
C1	C3	O1	H31	125.2°	120.0°
C1	C3	O1	H32	125.3°	120.0°
C1	C3	H31	H32	116.7°	120.0°
C3	C1	C6	N3	177.1°	180.0°
C3	C1	C6	H6	2.9°	0.0°
C1	C3	O1	P1	113.0°	180.0°
C6	C1	C2	N1	177.4°	180.0°
C6	C1	C2	N2	3.1°	0.3°
C6	C1	C3	O1	94.6°	0.1°
C6	C1	C3	H31	140.2°	120.1°
C6	C1	C3	H32	30.7°	120.0°
C1	C6	N3	C4	1.6°	0.0°
C1	C6	N3	H6	180.0°	180.0°
C2	N1	HN11	HN12	132.7°	180.0°
N1	C2	N2	C4	179.7°	179.8°
N2	C2	N1	HN11	124.9°	0.3°
N2	C2	N1	HN12	0.4°	179.7°
C2	N2	C4	C5	172.6°	179.7°
C2	N2	C4	N3	3.1°	0.5°
O1	C3	H31	H32	116.7°	120.0°
C3	O1	P1	O2	141.6°	180.0°
C3	O1	P1	O3	38.9°	60.0°
C3	O1	P1	O4	95.9°	60.0°
H31	C3	O1	P1	12.2°	60.0°
H32	C3	O1	P1	121.7°	60.0°
N2	C4	C5	N3	175.8°	179.8°
N2	C4	C5	H51	54.7°	90.3°
N2	C4	C5	H52	180.0°	29.7°
N2	C4	C5	H53	54.7°	149.7°
N2	C4	N3	C6	4.2°	0.2°
C4	C5	H51	H52	130.0°	120.0°
C4	C5	H51	H53	115.0°	119.9°
C4	C5	H52	H53	125.2°	120.0°
C5	C4	N3	C6	171.4°	180.0°
N3	C4	C5	H51	121.1°	89.9°
N3	C4	C5	H52	4.2°	150.1°
N3	C4	C5	H53	129.4°	30.0°
C4	N3	C6	H6	178.4°	180.0°
H51	C5	H52	H53	109.4°	120.0°
O1	P1	O2	O3	114.5°	120.0°
O1	P1	O2	O4	119.5°	120.0°
O1	P1	O3	O4	134.2°	120.0°
O1	P1	O2	HO2	180.0°	180.0°
O1	P1	O4	HO4	180.0°	60.0°
O2	P1	O3	O4	127.7°	120.0°
O2	P1	O4	HO4	72.2°	60.0°
O3	P1	O2	HO2	65.5°	60.0°
O3	P1	O4	HO4	46.1°	180.0°
O4	P1	O2	HO2	60.5°	60.0°

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PDB entries from 2026-02-11

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