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Crystal structure of streptokinase domain B

Analyse Crystal structure of streptokinase domain B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QQR
Type: protein
Length: 547 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Streptokinase domain B
UniProt: P00779
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Streptokinase domain B	protein	138	11% helix, 43% strand	P00779
B	Streptokinase domain B	protein	133	11% helix, 44% strand	P00779

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	972	0.81	0.83	91	empty
2	396	0.69	0.81	47	empty
3	210	0.61	0.82	29	empty
4	285	0.61	0.80	34	empty
5	101	0.46	0.79	16	empty

Interfaces

5 interfaces between chains.

A–D · 1499 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 603 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 533 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 401 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 335 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1QQR · Crystal structure of streptokinase domain B · the same entry in another collection · chain A against A, TM-score 1.00
P00779 · AlphaFold monomer V2.0 prediction for streptokinase C (P00779) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P00779
Elsewhere: RCSB PDB 1QQR · PDBe 1QQR · UniProt P00779

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