Research workbench

Human Fab fragment 5H2 against nhba from neisseria meningitidis

Analyse Human Fab fragment 5H2 against nhba from neisseria meningitidis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NYX
Type: protein
Length: 1,291 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain; Light chain
Ligands: SO4
Pockets: 14 · best druggability 0.65

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, O	Heavy chain	protein	224	9% helix, 53% strand	—
L	Light chain	protein	211	6% helix, 52% strand	—
M	Heavy chain	protein	223	12% helix, 53% strand	—
N	Light chain	protein	210	6% helix, 52% strand	—
P	Light chain	protein	199	7% helix, 52% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains H, L, P
GOL · Glycerol · additive · 12 copies · chains H, L, M, N, O, P

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

Pockets

14 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	248	0.65	0.83	26	empty
2	506	0.65	0.77	50	empty
3	620	0.63	0.74	89	empty
4	241	0.59	0.80	40	empty
5	189	0.55	0.79	30	GOL

Interfaces

11 interfaces between chains.

O–P · 1883 Å² buried · 20 hydrogen bonds · protein-protein
H–L · 1859 Å² buried · 17 hydrogen bonds · protein-protein
M–N · 1854 Å² buried · 17 hydrogen bonds · protein-protein
H–O · 873 Å² buried · 16 hydrogen bonds · protein-protein
L–M · 511 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide (disulfide).

Compared structures

5NYX · human Fab fragment 5H2 against NHBA from Neisseria meningitidis · the same entry in another collection · chain H against H, 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 5NYX · PDBe 5NYX

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