Protein Detail

Protein Information

PDBId & Chain	5AG8 : A
Molecule	Gingipain R2
Residues	149
Sequence
SSE Sequence^*(13)	`EEEEEEEEEEEEE`

^* Secondary structure Elements (SSE) from N to C terminal of the PDB chain. [SSE: H ("Alpha Helix"); E ("Strands")]

Protein Topology

Topology Information

Protein topology is represented by contact and orientation of secondary structure elements (SSEs). The figure on the left represents the contact map with information on type of orientation two SSEs share (color coded). The matrix can be represented in following string representation.

Contact String
cs [Click here to expand] `0.Ea.Ea.Ea.Ea.0.Ea.0.Ea.Ea.Ea.Ea-Ea.0.0.Ep.0.0.0.0.0.Ep.0-0.0.Ea.Ea.0.0.0.0.Ea.Ea-0.0.Ep.0.0.0.0.Ep.Ep-0.0.0.0.0.0.0.0-Ea.Ep.0.0.0.0.0-0.0.0.0.0.0-0.0.0.0.0-0.0.0.0-0.0.0-0.0-0`

Prefence of topology : False

[ Hover over the plot rectangles to know more about SSE-contact ]

Linear Topology Graph : 5AG8_A

Protein Id: 5AG8_A

Figure Detail - Blocks: Helix (rectangles), Strands (triangles); Colormap: Red (N-terminal),--(Green)-- Blue (C-Terminal). Spatial Connectivity by arc Lines [Hover over the image to know the SSE detail]

Topology Graph : 5AG8_A

Protein Id: 5AG8_A

Expand

Figure Detail - Blocks: Helix (circle), Strands (arrow); Colormap: Red (N-terminal), Blue (C-Terminal). Spatial Connectivity by dotted Lines [Hover over the image to know the SSE detail]

Modules in queried Topology

#SSE	SSE string	Contact String	Preferrence	ProteinDB	DomainsDB
3	EEE	0.Ea-Ea	False	3QTE:A, 3QTE:B, 3QTE:C, 5J4S:B, 2J5L:A,	d1bdsa_, d1ut3a_, d2j4wd1, d2nn6i2, 1bdsA00, 1bdsA00,
3	EEE	Ea.Ea-0	True	3FIF:F, 3MLQ:G, 4A94:C, 4EAG:B, 4EAI:B, 4OEL:B, 4PKF:C, 5BWD:C, 5DZD:A, 5K2M:E, 2BZY:A, 2QN5:B, 2V8Q:B,	d1co4a_, d1dl6a_, d1egfa_, d1gl1i_, d1k36a_, d1k81a_, d1ng2a1, d1nvpd2, d1pina1, d1tpga2, d1twfi1, d1twfi2, d2akla2, d2dara2, d2k4xa1, d2v8qb1, 1co4A00, 1dl6A00, 1co4A00, 1dl6A00, 1k36A00, 1nvpD02,
3	EEE	Ea.Ea-Ep	True	2XTT:A, 3CFA:L, 3CFA:M, 3CFA:R, 3CFA:S, 3CFH:L, 3CFH:M, 3CFH:R, 3CFH:S, 3LE4:A, 3MLQ:E, 3MLQ:H, 3TVJ:I, 4F98:A, 4GWT:A, 4N7F:A, 4N7F:B, 4REX:A, 5DZD:B, 5E24:B, 5E24:D, 1NH2:C, 1NVP:C, 2A50:A, 2HIP:A,	d1gl0i_, d1goia1, d1kbea_, d1mkna_, d1nh2c_, d1nh2d2, d1o9aa1, d1rl2a2, d2dk1a1, d2hipa_, d2ho2a1, d2jmfa1, 1kbeA00, 1mknA00, 1nh2C00, 1nvpC00, 1o9aA01,
3	EEE	Ea.0-0	True	2YFV:C, 2ZJR:U, 3B08:B, 3B08:E, 3B08:H, 3B08:K, 3D2Q:D, 3EGG:D, 3GL6:A, 3HVQ:D, 3KXY:Y, 3MMY:B, 3MMY:D, 3MMY:F, 3MMY:H, 3O7A:A, 3TND:D, 3TND:F, 3ZG9:A, 4EAZ:C, 4EAZ:D, 4LM6:A, 4LM6:C, 4LMS:A, 4LMX:A, 4LMX:C, 4LMX:E, 4LMX:G, 4LMX:I, 4LMX:K, 4MMS:A, 4MMS:C, 4MMS:E, 4Q4W:4, 4QF2:A, 4QF2:B, 4QF2:C, 4QF2:D, 4QF3:A, 4QF3:B, 4WJW:A, 5E4X:A, 5IYZ:E, 5KX5:E, 1D4M:4, 1G3J:B, 1HXS:4, 1J8E:A, 1JY2:O, 1VPZ:A, 1XG0:A, 1XG0:B, 1XU1:R, 2BTI:A,	d1cxxa2, d1k0ra4, d1lv3a_, d1wvka_, d1xg0a_, d1xpaa2, d1xu1r_, d1xu2r_, d2btia_, d2bv3a4, d2glia4, d2gtlm2, d2zjru1, d3ryce_, 1e0aB00, 1g3jD00, 1jy2O00, 1lv3A00, 1wvkA00, 1xg0B00, 2fyuI00, 2gliA04,
3	EEE	0.Ea-0	True	2Y8T:B, 2Y8T:E, 2ZJR:Z, 3H31:A, 3O27:B, 3SF4:D, 3SF4:E, 3SF4:F, 4I6M:D, 4XO1:A, 4YIZ:B, 4YIZ:D, 4YIZ:F, 5DM6:Z, 5ITM:A, 5ITM:B, 5ITM:C, 5ITM:D, 5ITM:E, 5ITM:F, 1AVY:A, 1HLQ:A, 1ICF:I, 1ISU:A, 1PML:A, 2ATC:B, 2DLB:A, 2GGV:A,	d1hlqa_, d1icfi_, d1isua_, d1ppji_, d1rwsa_, d1skza1, d1tdha3, d1yfba1, d2dlba1, d2i9aa2, d2qam01, d2zdra1, d3h31a_, 1avyA00, 1avyB00, 1avyA00, 1avyB00, 1hlqA00, 1icfI00, 1ppjI00, 1rwsA00, 2fd6A02,
4	EEEE	Ea.Ea.Ea-0.0-0	True	4A94:D, 5JB9:E, 1XDT:R,	d1autl1, d1auua_, d1eaic_, d1g1ta2, d1hx2a_, d1ijqa2, d1m7ja2, d1nzia2, d1szba2, d1tfia_, d1xdtr_, d2bz6l_, d2y5fl_, d3bpse1, 1auuA00, 1auuA00, 1eaiC00, 1hx2A00, 1moxD00, 1nziB02, 1ridA03, 1tfiA00, 1wj2A00, 2bz6L00,
4	EEEE	Ea.Ea.Ea-0.Ep-Ea	True	3TBN:A, 4BV4:L, 4LXR:K, 5AOQ:L, 5AOQ:M,	d1jmab2, 1ccvA00, 1ccvA00,
4	EEEE	Ea.0.Ea-0.0-0	True	3BG4:D, 3UA0:A, 3UCI:A, 4R5R:A, 4R5R:B, 4ZRP:C, 4ZRP:D, 5B4Y:B, 5C13:A, 5C13:G, 5F0E:B, 5F86:B, 5JQP:B, 5KXH:B, 5KY0:B, 5KY4:B, 1J2L:A, 1KIG:L, 1LSL:A, 2QSK:A, 2W2N:E,	d1ataa_, d1b9wa2, d1i07a_, d1j2la_, d1jmab1, d1ppqa_, d1q4ga2, d2i9aa1, d2j01y1, d2qqra2, 1eqgA01, 1fycA00, 1i07A00, 1xkbA01, 2fd6A01,
4	EEEE	0.Ea.0-0.0-0	True	2YNZ:A, 2YNZ:B, 2YNZ:C, 3C9I:A, 3C9I:B, 3C9I:C, 3C9I:D, 3C9I:E, 3C9I:F, 3ZMF:C, 5BU5:A, 5BU5:B, 5BU5:C, 5BU5:D, 5BU5:E, 5BU5:F, 5BU8:A, 5BU8:B,
4	EEEE	0.Ea.Ea-0.0-0	True	2YH9:A, 2YH9:B, 2YH9:C, 3OW2:Z, 3UL5:C, 4YX1:A, 4YX1:B, 5U6Z:A, 1VQO:1, 2QRD:B,	d1vq811, d2f1la1, d2qlvb2, 1vq8100, 2f1lA02,
4	EEEE	Ea.Ea.Ea-Ep.0-Ea	False	4YX7:A, 4YX7:D, 5HCC:D, 5HCD:D,
5	EEEEE	Ea.Ea.0.Ea-Ep.0.0-Ea.0-0	False	2PKA:A,
5	EEEEE	Ea.0.Ea.0-0.0.0-0.0-0	True	3TND:B, 3TND:H, 3ZVK:E, 3ZVK:F, 3ZVK:G, 3ZVK:H, 5K8J:A, 5K8J:D,	d2qqra1,
5	EEEEE	Ea.0.Ea.Ea-0.0.0-0.0-0	False	1R8O:A,	d1v0ea2,
6	EEEEEE	Ea.Ea.Ea.0.Ea-0.Ep.0.0-Ea.Ea.0-Ep.0-0	False	3FCG:B,
6	EEEEEE	Ea.0.Ea.0.Ea-0.0.0.0-0.0.0-0.0-0	True	3C05:A, 3C05:B, 3C05:C, 3C05:D, 3X3F:A, 4GNE:A, 4KU0:D, 5TLK:X, 1KI0:A, 1RMR:A, 1TEJ:A,

Protein In ProLegoDB with identical/similar Topology

Proteins with Identical Topology

[Same secondary structure composition, contact-pair and orientation]

PDB Id	Chain	Residues	Molecule	Detail Topology
5AG8	B	149	Gingipain R2	View

Protein with similar Topology [same scaffold]

[Same secondary structure composition and contact-pair but of different orientation]

PDB Id	Chain	Residues	Molecule	Detail Topology

Proteins with topologies of same secondary structure (H/E) component

[Topologies with same secondary structure composition with different contact-pairs and orientation]

PDB Id	Chain	Residues	Molecule	Detail Topology
2X55	A	274	Coagulase/fibrinolysin	View
2XBT	A	158	Cellulosomal scaffoldin	View
2XC8	A	118	Uncharacterized protein	View
2XC8	B	124	Uncharacterized protein	View
2YYO	A	157	SPRY domain-containing protein 3	View
2Z5W	A	136	BclA protein	View
2ZHN	A	145	Galectin-9	View
3A07	A	116	Actinohivin	View
3A07	B	118	Actinohivin	View
3AP9	A	151	Galectin-8	View
3APA	A	138	Zymogen granule membrane protein 16	View
3BWR	C	267	Major capsid protein VP1	View
3BWR	D	265	Major capsid protein VP1	View
3BX1	C	181	Alpha-amylase/subtilisin inhibitor	View
3BX1	D	181	Alpha-amylase/subtilisin inhibitor	View
3C0D	F	103	Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein	View
3D4R	B	152	Uncharacterized protein	View
3D4R	D	153	Uncharacterized protein	View
3D4R	F	153	Uncharacterized protein	View
3DDY	A	175	Lumazine protein	View
3DUR	A	106	Aberrantly recombined kappa chain Vk8/J1 region	View
3DUR	C	106	Aberrantly recombined kappa chain Vk8/J1 region	View
3E5T	A	228	Red fluorescent protein eqFP611	View
3EJK	A	155	Polysaccharide biosynthesis domain-containing protein	View
3ETP	A	187	Ephrin type-B receptor 2	View
3F62	B	145	Interleukin-18	View
3G7M	A	151	Xylanase inhibitor TL-XI	View
3GF6	A	214	Uncharacterized protein	View
3ISY	A	115	Intracellular proteinase inhibitor	View
3N6Y	A	121	Uncharacterized protein	View
3N6Y	B	120	Uncharacterized protein	View
3NBC	A	148	Ricin B-like lectin	View
3PIB	A	226	eqFP578 fluorescent protein	View
3PIB	B	235	eqFP578 fluorescent protein	View
3PIB	C	225	eqFP578 fluorescent protein	View
3PIB	D	227	eqFP578 fluorescent protein	View
3PVE	B	172	Agrin	View
3R0R	A	194	Putative capsid protein	View
3RKD	A	146	Capsid protein	View
3RKD	B	145	Capsid protein	View
3TGX	E	207	Interleukin-21 receptor	View
3TWI	A	136	Uncharacterized protein	View
3TWI	B	136	Uncharacterized protein	View
3TWI	C	136	Uncharacterized protein	View
3VWC	A	146	Serine protease inhibitor 1	View
3WMV	A	150	Lectin	View
3WMV	B	149	Lectin	View
3ZO0	B	180	E3 ubiquitin-protein ligase TRIM21	View
4AKM	B	157	Lysosome-associated membrane glycoprotein 3	View
4BH5	B	130	Murein hydrolase activator EnvC	View
4BH5	C	130	Murein hydrolase activator EnvC	View
4BH5	D	130	Murein hydrolase activator EnvC	View
4BZ4	A	198	Uncharacterized protein	View
4BZ4	B	203	Uncharacterized protein	View
4BZ4	C	198	Uncharacterized protein	View
4BZ4	D	197	Uncharacterized protein	View
4BZ4	E	203	Uncharacterized protein	View
4BZ4	F	198	Uncharacterized protein	View
4D7Y	A	131	C1q-related factor	View
4DT5	A	143	Antifreeze protein	View
4DT5	B	138	Antifreeze protein	View
4EKX	B	142	Interleukin-18	View
4EKX	D	155	Interleukin-18	View
4F8L	A	138	pH 6 antigen	View
4GAF	A	152	Interleukin-1 beta	View
4GAI	A	152	Interleukin-1 beta	View
4GAI	B	140	Interleukin-1 beta	View
4ITC	A	170	Lys-gingipain W83	View
4J8Q	A	191	Uncharacterized protein	View
4MBY	A	277	Major capsid protein VP1	View
4MJ0	A	265	Major capsid protein VP1	View
4MJ0	B	263	Major capsid protein VP1	View
4MJ0	C	247	Major capsid protein VP1	View
4MJ0	D	267	Major capsid protein VP1	View
4MJ0	E	264	Major capsid protein VP1	View
4NZD	A	210	Interleukin-21 receptor	View
4NZD	C	210	Interleukin-21 receptor	View
4O1R	A	142	Replicative DNA helicase	View
4OHS	A	219	Blue chromoprotein aeCP597	View
4OHS	B	225	Blue chromoprotein aeCP597	View
4OHS	C	221	Blue chromoprotein aeCP597	View
4OHS	D	217	Blue chromoprotein aeCP597	View
4OHS	E	217	Blue chromoprotein aeCP597	View
4OHS	F	225	Blue chromoprotein aeCP597	View
4OHS	G	214	Blue chromoprotein aeCP597	View
4OHS	H	216	Blue chromoprotein aeCP597	View
4OZF	G	193	TRA@ protein	View
4P9I	A	163	Ryanodine receptor 2	View
4P9J	A	180	Ryanodine receptor 1	View
4P9J	C	180	Ryanodine receptor 1	View
4PHX	B	130	Protein AggB	View
4PHX	D	132	Protein AggB	View
4PHX	F	126	Protein AggB	View
4POS	A	270	VP1	View
4POS	B	270	VP1	View
4POS	C	269	VP1	View
4POS	D	271	VP1	View
4POS	E	270	VP1	View
4POS	F	272	VP1	View
4POS	G	270	VP1	View
4POS	H	271	VP1	View
4POS	I	272	VP1	View
4POS	J	274	VP1	View
4Q27	A	130	Galectin-1	View
4Q27	B	130	Galectin-1	View
4QB6	A	129	Xyn30D	View
4U60	A	271	VP1	View
4U60	B	262	VP1	View
4U60	C	274	VP1	View
4U60	D	268	VP1	View
4U60	E	271	VP1	View
4UXA	A	131	Cupin 2 conserved barrel domain protein	View
4UXA	B	131	Cupin 2 conserved barrel domain protein	View
4UXA	C	131	Cupin 2 conserved barrel domain protein	View
4UXA	D	131	Cupin 2 conserved barrel domain protein	View
4UXA	E	131	Cupin 2 conserved barrel domain protein	View
4UXA	F	131	Cupin 2 conserved barrel domain protein	View
4UXA	G	131	Cupin 2 conserved barrel domain protein	View
4UXA	I	131	Cupin 2 conserved barrel domain protein	View
4UXA	K	131	Cupin 2 conserved barrel domain protein	View
4UXA	L	131	Cupin 2 conserved barrel domain protein	View
4UXA	M	131	Cupin 2 conserved barrel domain protein	View
4UXA	O	131	Cupin 2 conserved barrel domain protein	View
4UXA	Q	131	Cupin 2 conserved barrel domain protein	View
4UXA	S	131	Cupin 2 conserved barrel domain protein	View
4UYP	A	144	Cellulosomal scaffoldin anchoring protein C	View
4UYP	C	146	Cellulosomal scaffoldin anchoring protein C	View
4WVV	A	145	Galectin	View
4X0Y	A	258	VP1 capsid protein	View
4X0Y	B	257	VP1 capsid protein	View
4X0Y	C	257	VP1 capsid protein	View
4X0Y	D	257	VP1 capsid protein	View
4X0Y	E	259	VP1 capsid protein	View
4XZP	A	148	Galectin-4	View
4ZB1	B	226	Blue chromoprotein, sgBP	View
4ZGI	A	135	TRAF-interacting protein with FHA domain-containing protein A	View
4ZZF	A	146	Basal-body rod modification protein FlgD	View
5CIR	A	149	Tumor necrosis factor ligand superfamily member 10	View
5CIR	B	151	Tumor necrosis factor ligand superfamily member 10	View
5CIR	D	150	Tumor necrosis factor ligand superfamily member 10	View
5EHA	A	153	Lectin-like fold protein	View
5EIQ	A	188	Osteoclast-associated immunoglobulin-like receptor	View
5F8S	A	149	GalNAc/Gal-specific lectin	View
5F8S	B	149	GalNAc/Gal-specific lectin	View
5GV0	A	162	Lysosome-associated membrane glycoprotein 1	View
5GZC	A	152	Galectin-8	View
5GZD	A	148	Galectin-8	View
5GZG	A	149	Galectin-8	View
5JMC	D	92	Synaptic vesicle glycoprotein 2C	View
5JR2	A	179	Ephrin type-A receptor 4	View
5JR2	B	179	Ephrin type-A receptor 4	View
5JR2	C	175	Ephrin type-A receptor 4	View
5JR2	D	176	Ephrin type-A receptor 4	View
5LNG	C	145	Hypothetical fimbrial-like protein ydeQ	View
5MX0	A	304	Fibromodulin	View
5MX0	B	306	Fibromodulin	View
5TU8	A	132	Accumulation associated protein	View
5TU9	A	139	Accumulation associated protein	View
8I1B	A	146	Interleukin-1 beta	View
1D2S	A	170	Sex hormone-binding globulin	View
1DYO	A	153	Endo-1,4-beta-xylanase Y	View
1EEQ	A	107	Ig kappa chain V-IV region	View
1EK3	A	108	Ig kappa chain V-IV region	View
1I8A	A	189	Endo-1,4-beta-xylanase A	View
1KXG	A	144	Tumor necrosis factor ligand superfamily member 13B	View
1MI8	A	141	Replicative DNA helicase	View
1MVU	A	112	ScFv B8E5 protein	View
1NZI	A	155	Complement C1s subcomponent	View
1QMJ	A	132	16 kDa beta-galactoside-binding lectin	View
1SLT	A	130	Galectin-1	View
1UXZ	A	131	Cellulase B	View
1V0A	A	165	Endoglucanase H	View
1WBA	A	171	Albumin-1	View
1YQ5	A	142	Spike protein P5	View
2D6M	A	151	Galectin-9	View
2IWG	B	181	E3 ubiquitin-protein ligase TRIM21	View
2NVH	A	152	Interleukin-1 beta	View
2OTP	A	193	Leukocyte immunoglobulin-like receptor subfamily A member 2	View
5GZF	A	150	Galectin-8	View

Topology view of query protein [ProLego results]

5AG8 : A

Topology Information