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Crystal structure of sbnh in complex with the cofactor plp, a plp- dependent decarboxylase in staphyloferrin B biothesynthesis

Analyse Crystal structure of sbnh in complex with the cofactor plp, a plp- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KNI
Type: protein
Length: 1,145 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable diaminopimelate decarboxylase protein
UniProt: A0A0H3JPF2
Ligands: PLP
Pockets: 12 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable diaminopimelate decarboxylase protein	protein	381	35% helix, 28% strand	A0A0H3JPF2
B	Probable diaminopimelate decarboxylase protein	protein	381	36% helix, 27% strand	A0A0H3JPF2
C	Probable diaminopimelate decarboxylase protein	protein	383	35% helix, 28% strand	A0A0H3JPF2

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	636	0.80	0.85	89	PLP
2	491	0.67	0.78	59	empty
3	438	0.62	0.76	45	empty
4	143	0.59	0.84	23	empty
5	167	0.58	0.82	29	empty

Interfaces

3 interfaces between chains.

A–B · 3090 Å² buried · 46 hydrogen bonds · protein-protein
B–C · 627 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 11 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).

Compared structures

6KNI · Crystal structure of SbnH in complex with the cofactor PLP, a PLP-dependent decarboxylase… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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Every structure of UniProt A0A0H3JPF2
Elsewhere: RCSB PDB 6KNI · PDBe 6KNI · UniProt A0A0H3JPF2

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