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Structure of periplasmic binding protein bugd

Analyse Structure of periplasmic binding protein bugd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F5X
Type: protein
Length: 898 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bugd
Ligands: ASP
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Bugd	protein	299	43% helix, 21% strand	—
B	Bugd	protein	300	43% helix, 21% strand	—

Ligands and binding sites

ASP · Aspartic acid · ligand · 3 copies · chains A, B, C

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

Pockets

6 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	555	0.74	0.81	50	empty
2	519	0.73	0.82	46	empty
3	313	0.53	0.74	44	empty
4	318	0.51	0.73	41	empty
5	91	0.36	0.75	18	empty

Interfaces

2 interfaces between chains.

A–C · 538 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 495 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 modified, 3 disulfide (engineered, disulfide).

Compared structures

2F5X · Structure of periplasmic binding protein BugD · the same entry in another collection · chain B against B, 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
Elsewhere: RCSB PDB 2F5X · PDBe 2F5X

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