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Human beta-defensin 2

Analyse Human beta-defensin 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1FD4
Type: protein
Length: 656 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-defensin 2
UniProt: O15263
Ligands: SO4
Pockets: 17 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	Beta-defensin 2	protein	41	15% helix, 39% strand	O15263

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, E, F, I, M, N

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

Pockets

17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	535	0.77	0.84	67	empty
2	466	0.75	0.84	73	empty
3	173	0.43	0.73	26	empty
4	136	0.41	0.75	31	empty
5	160	0.40	0.73	41	empty

Interfaces

44 interfaces between chains.

E–F · 622 Å² buried · 3 hydrogen bonds · protein-protein
G–H · 581 Å² buried · 3 hydrogen bonds · protein-protein
I–J · 555 Å² buried · 3 hydrogen bonds · protein-protein
O–P · 528 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 526 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 disulfide (disulfide).

Compared structures

1FD4 · Human beta-defensin 2 · the same entry in another collection · chain K against K, 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 O15263
Elsewhere: RCSB PDB 1FD4 · PDBe 1FD4 · UniProt O15263

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