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Anti CMV Fab fragment

Analyse Anti CMV Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LRI
Type: protein
Length: 879 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Msl-109 light chain; Msl-109 heavy chain
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Msl-109 light chain	protein	217	6% helix, 51% strand	—
P	Msl-109 heavy chain	protein	222	7% helix, 50% strand	—
C	Msl-109 heavy chain	protein	223	6% helix, 50% strand	—

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	868	0.74	0.78	81	empty
2	529	0.60	0.74	57	empty
3	299	0.57	0.77	46	empty
4	113	0.43	0.78	24	empty
5	116	0.37	0.74	26	empty

Interfaces

5 interfaces between chains.

A–P · 1941 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1888 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 451 Å² buried · 5 hydrogen bonds · protein-protein
P–C · 99 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 40 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4LRI · Anti CMV Fab Fragment · the same entry in another collection · chain A against A, 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 4LRI · PDBe 4LRI

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