MolNFT v1 · #102678 · protein

Structural basis for the recognition of human cytomegalovirus glycoprotein B by the neutralizing human antibody SM5-1

4OT1 · Envelope glycoprotein B: “Structural basis for the recognition of human cytomegalovirus glycoprotein B by the neutralizing human…”. X-ray diffraction, 7 pockets (best druggability 0.59). MolNFT v1 #102678 on GenesisL1: 3D structure…

PDB: 4OT1
Type: protein
Length: 559 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein B; SM5-1 Fab heavy chain; SM5-1 Fab light chain
UniProt: P13201
Pockets: 7 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Envelope glycoprotein B	protein	113	16% helix, 49% strand	P13201
H	SM5-1 Fab heavy chain	protein	232	8% helix, 53% strand	—
L	SM5-1 Fab light chain	protein	214	7% helix, 51% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 3 copies · chains A, H, L
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains L

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	215	0.59	0.81	27	empty
2	306	0.55	0.75	32	EDO
3	235	0.48	0.74	34	empty
4	126	0.44	0.77	29	empty
5	78	0.40	0.79	25	empty

Interfaces

3 interfaces between chains.

H–L · 1747 Å² buried · 12 hydrogen bonds · protein-protein
A–H · 537 Å² buried · 13 hydrogen bonds · protein-protein
A–L · 282 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4OT1 · Structural Basis for the Recognition of Human Cytomegalovirus Glycoprotein B by the… · 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 P13201
Elsewhere: RCSB PDB 4OT1 · PDBe 4OT1 · UniProt P13201

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