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Cryo-EM structure of the hcmv pentamer bound by fabs 2-18 and 8I21

Analyse Cryo-EM structure of the hcmv pentamer bound by fabs 2-18 and 8I21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KBB
Type: protein
Length: 812 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-18 Fab heavy chain; 2-18 Fab light chain; Envelope protein UL128; Envelope glycoprotein…
UniProt: C8BLJ3, A0A0G2TB82, Q38M21
Pockets: 8 · best druggability 0.59

Structure

electron microscopy · 7 distinct chains · 15% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-18 Fab heavy chain	protein	127	7% helix, 50% strand	—
B	2-18 Fab light chain	protein	107	3% helix, 50% strand	—
C	Envelope protein UL128	protein	70	26% helix, 16% strand	C8BLJ3
D	Envelope glycoprotein UL130	protein	170	27% helix, 35% strand	A0A0G2TB82
E	UL131A	protein	108	43% helix, 19% strand	Q38M21
H	8I21 Fab heavy chain	protein	122	0% helix, 53% strand	—
L	8I21 Fab light chain	protein	108	3% helix, 48% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	305	0.59	0.78	32	empty
2	151	0.48	0.78	27	empty
3	178	0.47	0.75	29	empty
4	71	0.38	0.78	16	empty
5	74	0.38	0.78	20	empty

Interfaces

12 interfaces between chains.

D–E · 2707 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 1025 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 971 Å² buried · 16 hydrogen bonds · protein-protein
D–L · 966 Å² buried · 14 hydrogen bonds · protein-protein
H–L · 917 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7KBB · Cryo-EM structure of the HCMV pentamer bound by Fabs 2-18 and 8I21 · 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
Every structure of UniProt C8BLJ3
Every structure of UniProt A0A0G2TB82
Every structure of UniProt Q38M21
Elsewhere: RCSB PDB 7KBB · PDBe 7KBB · UniProt C8BLJ3 · UniProt A0A0G2TB82 · UniProt Q38M21

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