English 日本語简体中文繁體中文 한국어

✖

Menu

RCSB PDB PDBe BMRB Adv. Search Search help

Summary Geometry Related PDB entries

SXS

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O1	C2	doub	1.22Å	1.21Å
C2	N3	sing	1.34Å	1.39Å
C2	C4	sing	1.47Å	1.48Å
N3	S13	sing	1.67Å	1.60Å
C4	C5	doub	1.41Å	1.36Å	Aromatic
C4	C12	sing	1.40Å	1.34Å	Aromatic
C5	C6	sing	1.37Å	1.38Å	Aromatic
C6	C7	doub	1.39Å	1.39Å	Aromatic
C7	N8	sing	1.39Å	1.35Å
C7	C11	sing	1.40Å	1.36Å	Aromatic
C11	C12	doub	1.36Å	1.33Å	Aromatic
C12	S13	sing	1.77Å	1.71Å
S13	O14	doub	1.42Å	1.47Å
S13	O15	doub	1.42Å	1.46Å
N3	HN3	sing	0.97Å	1.00Å
C5	H5	sing	1.08Å	1.08Å
C6	H6	sing	1.08Å	1.08Å
N8	HN8	sing	0.97Å	1.00Å
N8	HN8A	sing	0.97Å	1.00Å
C11	H11	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	C2	N3	125.9°	120.9°
O1	C2	C4	118.3°	121.0°
N3	C2	C4	114.8°	118.1°
C2	N3	S13	107.2°	105.9°
C2	N3	HN3	126.4°	127.1°
C2	C4	C5	129.7°	129.9°
C2	C4	C12	108.9°	112.5°
N3	S13	C12	98.3°	99.8°
N3	S13	O14	114.0°	107.6°
N3	S13	O15	110.5°	107.6°
S13	N3	HN3	126.4°	127.0°
C5	C4	C12	121.3°	117.6°
C4	C5	C6	113.0°	120.4°
C4	C5	H5	123.5°	119.8°
C4	C12	C11	129.8°	122.1°
C4	C12	S13	110.0°	103.7°
C5	C6	C7	121.1°	120.8°
C6	C5	H5	123.5°	119.8°
C5	C6	H6	119.4°	119.5°
C6	C7	N8	111.4°	120.3°
C6	C7	C11	125.7°	119.4°
C7	C6	H6	119.5°	119.6°
N8	C7	C11	122.7°	120.3°
C7	N8	HN8	109.5°	120.0°
C7	N8	HN8A	109.5°	120.0°
C7	C11	C12	108.7°	119.7°
C7	C11	H11	125.7°	120.1°
C11	C12	S13	120.0°	134.2°
C12	C11	H11	125.6°	120.2°
C12	S13	O14	106.5°	107.6°
C12	S13	O15	108.4°	107.3°
O14	S13	O15	117.1°	124.2°
HN8	N8	HN8A	109.4°	120.1°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C2	N3	C4	168.5°	179.8°
O1	C2	N3	S13	176.8°	179.9°
O1	C2	C4	C5	3.3°	0.1°
O1	C2	C4	C12	173.4°	180.0°
O1	C2	N3	HN3	3.2°	0.1°
C2	N3	S13	HN3	180.0°	180.0°
N3	C2	C4	C5	172.7°	179.8°
N3	C2	C4	C12	4.0°	0.2°
C2	N3	S13	C12	8.2°	0.2°
C2	N3	S13	O14	120.5°	112.0°
C2	N3	S13	O15	105.1°	112.0°
C4	C2	N3	S13	8.4°	0.2°
C2	C4	C5	C12	176.4°	180.0°
C2	C4	C5	C6	176.7°	179.9°
C2	C4	C12	C11	173.2°	180.0°
C2	C4	C12	S13	2.1°	0.1°
C4	C2	N3	HN3	171.7°	179.7°
C2	C4	C5	H5	3.3°	0.1°
N3	S13	C12	C4	6.3°	0.0°
N3	S13	C12	C11	169.5°	179.8°
N3	S13	C12	O14	118.1°	112.1°
N3	S13	C12	O15	115.0°	112.0°
N3	S13	O14	O15	131.2°	126.7°
C4	C5	C6	H5	180.0°	179.9°
C4	C5	C6	C7	4.6°	0.1°
C5	C4	C12	C11	3.9°	0.0°
C5	C4	C12	S13	179.1°	179.9°
C4	C5	C6	H6	175.4°	180.0°
C12	C4	C5	C6	0.3°	0.0°
C4	C12	C11	C7	2.9°	0.0°
C4	C12	C11	S13	174.8°	179.9°
C4	C12	S13	O14	124.5°	112.1°
C4	C12	S13	O15	108.6°	112.0°
C12	C4	C5	H5	179.7°	179.9°
C4	C12	C11	H11	177.1°	180.0°
C5	C6	C7	H6	180.0°	179.9°
C5	C6	C7	N8	177.9°	180.0°
C5	C6	C7	C11	5.9°	0.1°
C6	C7	N8	C11	176.4°	180.0°
C6	C7	C11	C12	1.9°	0.0°
C7	C6	C5	H5	175.4°	180.0°
C6	C7	N8	HN8	180.0°	0.0°
C6	C7	N8	HN8A	60.0°	179.9°
C6	C7	C11	H11	178.0°	180.0°
N8	C7	C11	C12	177.8°	180.0°
N8	C7	C6	H6	2.1°	0.0°
C7	N8	HN8	HN8A	120.0°	179.9°
N8	C7	C11	H11	2.2°	0.0°
C7	C11	C12	H11	180.0°	180.0°
C7	C11	C12	S13	177.8°	179.9°
C11	C7	C6	H6	174.2°	180.0°
C11	C7	N8	HN8	3.6°	180.0°
C11	C7	N8	HN8A	116.4°	0.0°
C11	C12	S13	O14	51.3°	68.0°
C11	C12	S13	O15	75.6°	67.8°
C12	S13	O14	O15	121.5°	126.5°
C12	S13	N3	HN3	171.8°	179.8°
S13	C12	C11	H11	2.2°	0.2°
O14	S13	N3	HN3	59.5°	68.0°
O15	S13	N3	HN3	74.9°	68.0°
H5	C5	C6	H6	4.5°	0.1°

219869

PDB entries from 2024-05-15

PDB statistics

PDBj update info

Contact PDBj

numon