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BC1 fragment of streptococcal M1 protein in complex with human fibrinogen

Analyse BC1 fragment of streptococcal M1 protein in complex with human fibrinogen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XNX
Type: protein
Length: 2,959 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibrinogen alpha chain; Fibrinogen beta chain; Fibrinogen gamma chain; M protein
UniProt: P02671, P02675, P02679, Q48WD8
Pockets: 20 · best druggability 0.62

Structure

x-ray diffraction · 13 distinct chains · 25% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fibrinogen alpha chain	protein	74	50% helix, 1% strand	P02671
B	Fibrinogen beta chain	protein	312	19% helix, 23% strand	P02675
C	Fibrinogen gamma chain	protein	302	20% helix, 19% strand	P02679
D	Fibrinogen alpha chain	protein	76	54% helix, 0% strand	P02671
E	Fibrinogen beta chain	protein	309	17% helix, 22% strand	P02675
F	Fibrinogen gamma chain	protein	303	26% helix, 18% strand	P02679
G	Fibrinogen alpha chain	protein	72	53% helix, 1% strand	P02671
H	Fibrinogen beta chain	protein	313	19% helix, 24% strand	P02675
I	Fibrinogen gamma chain	protein	300	22% helix, 21% strand	P02679
J	Fibrinogen alpha chain	protein	72	38% helix, 1% strand	P02671
K	Fibrinogen beta chain	protein	308	16% helix, 24% strand	P02675
L	Fibrinogen gamma chain	protein	304	20% helix, 21% strand	P02679
M, N	M protein	protein	107	80% helix, 0% strand	Q48WD8

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	164	0.62	0.84	27	empty
2	323	0.59	0.77	38	empty
3	161	0.58	0.82	26	empty
4	314	0.58	0.77	34	empty
5	325	0.58	0.76	34	empty

Interfaces

29 interfaces between chains.

M–N · 2656 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 2399 Å² buried · 29 hydrogen bonds · protein-protein
K–L · 2298 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2239 Å² buried · 23 hydrogen bonds · protein-protein
H–I · 2220 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

2XNX · BC1 fragment of streptococcal M1 protein in complex with human fibrinogen · the same entry in another collection · chain I against I, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P02671
Every structure of UniProt P02675
Every structure of UniProt P02679
Every structure of UniProt Q48WD8
Elsewhere: RCSB PDB 2XNX · PDBe 2XNX · UniProt P02671 · UniProt P02675 · UniProt P02679 · UniProt Q48WD8

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