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Crystal structure of hcmv gb-neutralizing SM5-1 Fab fragment

Analyse Crystal structure of hcmv gb-neutralizing SM5-1 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OSU
Type: protein
Length: 435 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SM5-1 Fab heavy chain; SM5-1 Fab light chain
Ligands: NA
Pockets: 6 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	SM5-1 Fab heavy chain	protein	223	8% helix, 52% strand	—
L	SM5-1 Fab light chain	protein	212	9% helix, 51% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains H
FMT · Formic acid · additive · 7 copies · chains H, L

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

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	121	0.44	0.77	22	empty
2	52	0.35	0.79	14	empty
3	127	0.35	0.72	31	empty
4	50	0.32	0.78	19	empty
5	63	0.32	0.76	15	empty

Interfaces

1 interface between chains.

H–L · 1590 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4OSU · Crystal structure of HCMV gB-neutralizing SM5-1 Fab fragment · 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 4OSU · PDBe 4OSU

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