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Summary Geometry Related PDB entries

4ZD

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
S06	C05	sing	1.76Å	1.72Å
S06	C07	sing	1.76Å	1.77Å
C04	C05	doub	1.35Å	1.34Å
C04	C02	sing	1.41Å	1.48Å
C02	O01	doub	1.22Å	1.37Å
C02	O03	sing	1.35Å	1.23Å
C07	C08	doub	1.39Å	1.41Å	Aromatic
C07	C12	sing	1.39Å	1.40Å	Aromatic
C08	C09	sing	1.38Å	1.40Å	Aromatic
C12	C11	doub	1.38Å	1.40Å	Aromatic
C09	C10	doub	1.38Å	1.40Å	Aromatic
C11	C10	sing	1.38Å	1.39Å	Aromatic
C10	H1	sing	1.08Å	1.08Å
O03	H2	sing	0.97Å	0.95Å
C04	H3	sing	1.08Å	1.08Å
C05	H5	sing	1.08Å	1.08Å
C08	H7	sing	1.08Å	1.08Å
C09	H8	sing	1.08Å	1.08Å
C11	H9	sing	1.08Å	1.08Å
C12	H10	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C05	S06	C07	113.1°	100.0°
S06	C05	C04	123.8°	120.0°
S06	C05	H5	118.1°	120.0°
S06	C07	C08	120.9°	120.1°
S06	C07	C12	121.9°	120.0°
C05	C04	C02	121.2°	120.0°
C05	C04	H3	119.4°	120.0°
C04	C05	H5	118.1°	120.0°
C04	C02	O01	117.3°	120.0°
C04	C02	O03	127.0°	120.0°
C02	C04	H3	119.4°	120.0°
O01	C02	O03	114.4°	120.0°
C02	O03	H2	109.5°	114.0°
C08	C07	C12	117.2°	119.9°
C07	C08	C09	121.8°	119.9°
C07	C08	H7	119.1°	120.0°
C07	C12	C11	121.3°	119.9°
C07	C12	H10	119.4°	120.1°
C08	C09	C10	120.2°	120.1°
C09	C08	H7	119.1°	120.1°
C08	C09	H8	119.9°	120.0°
C12	C11	C10	120.8°	120.1°
C12	C11	H9	119.6°	120.0°
C11	C12	H10	119.4°	120.0°
C09	C10	C11	118.8°	120.1°
C09	C10	H1	120.6°	119.9°
C10	C09	H8	119.9°	119.9°
C11	C10	H1	120.6°	120.0°
C10	C11	H9	119.6°	119.9°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
S06	C05	C04	H5	180.0°	179.9°
S06	C05	C04	C02	117.6°	180.0°
C05	S06	C07	C08	127.8°	85.9°
C05	S06	C07	C12	52.8°	94.2°
S06	C05	C04	H3	62.4°	0.0°
C07	S06	C05	C04	86.9°	174.8°
S06	C07	C08	C12	179.4°	179.9°
S06	C07	C08	C09	179.4°	180.0°
S06	C07	C12	C11	179.4°	180.0°
C07	S06	C05	H5	93.1°	5.2°
S06	C07	C08	H7	0.6°	0.1°
S06	C07	C12	H10	0.6°	0.1°
C05	C04	C02	H3	180.0°	180.0°
C05	C04	C02	O01	89.4°	0.0°
C05	C04	C02	O03	76.9°	180.0°
C04	C02	O01	O03	168.0°	179.9°
C04	C02	O03	H2	166.6°	180.0°
C02	C04	C05	H5	62.4°	0.0°
O01	C02	O03	H2	0.0°	0.1°
O01	C02	C04	H3	90.6°	180.0°
O03	C02	C04	H3	103.1°	0.1°
C07	C08	C09	H7	180.0°	179.9°
C08	C07	C12	C11	0.0°	0.2°
C07	C08	C09	C10	0.0°	0.1°
C07	C08	C09	H8	179.9°	180.0°
C08	C07	C12	H10	180.0°	180.0°
C12	C07	C08	C09	0.1°	0.2°
C07	C12	C11	H10	180.0°	179.8°
C07	C12	C11	C10	0.2°	0.0°
C12	C07	C08	H7	179.9°	179.8°
C07	C12	C11	H9	179.8°	180.0°
C08	C09	C10	H8	180.0°	179.9°
C08	C09	C10	C11	0.2°	0.3°
C08	C09	C10	H1	179.8°	180.0°
C12	C11	C10	C09	0.3°	0.3°
C12	C11	C10	H9	180.0°	180.0°
C12	C11	C10	H1	179.7°	180.0°
C09	C10	C11	H1	180.0°	179.7°
C10	C09	C08	H7	180.0°	180.0°
C09	C10	C11	H9	179.7°	179.7°
C11	C10	C09	H8	179.8°	179.8°
C10	C11	C12	H10	179.8°	179.8°
H1	C10	C09	H8	0.3°	0.1°
H1	C10	C11	H9	0.3°	0.0°
H3	C04	C05	H5	117.6°	179.9°
H7	C08	C09	H8	0.1°	0.1°
H9	C11	C12	H10	0.2°	0.2°

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PDB entries from 2026-02-04

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