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Crystal structure of the hcmv pentamer-specific Fab 2-18

Analyse Crystal structure of the hcmv pentamer-specific Fab 2-18 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KBA
Type: protein
Length: 887 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-18 Fab heavy chain; 2-18 Fab light chain
Pockets: 9 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-18 Fab heavy chain	protein	230	8% helix, 50% strand	—
B, L	2-18 Fab light chain	protein	213	7% helix, 51% strand	—
H	2-18 Fab heavy chain	protein	231	4% helix, 49% strand	—

Pockets

9 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	673	0.69	0.77	65	empty
2	771	0.66	0.74	73	empty
3	511	0.65	0.77	64	empty
4	196	0.53	0.78	24	empty
5	89	0.39	0.78	19	empty

Interfaces

3 interfaces between chains.

H–L · 1966 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1932 Å² buried · 14 hydrogen bonds · protein-protein
B–L · 931 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 modified (disulfide, cyclization).

Compared structures

7KBA · Crystal structure of the HCMV pentamer-specific Fab 2-18 · 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 7KBA · PDBe 7KBA

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