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Crystal structure of yersinia pseudotuberculosis-derived mitogen (ypm)

Analyse Crystal structure of yersinia pseudotuberculosis-derived mitogen (ypm) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PM4
Type: protein
Length: 351 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ypm
UniProt: Q57221
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Ypm	protein	117	3% helix, 53% strand	Q57221

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	666	0.76	0.82	60	empty
2	50	0.46	0.85	14	empty
3	72	0.43	0.81	18	empty
4	76	0.29	0.73	20	empty

Interfaces

3 interfaces between chains.

A–B · 533 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 517 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 506 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1PM4 · Crystal structure of Yersinia pseudotuberculosis-derived mitogen (YPM) · the same entry in another collection · chain A against A, 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 Q57221
Elsewhere: RCSB PDB 1PM4 · PDBe 1PM4 · UniProt Q57221

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