MolNFT v1 · #114076 · protein

Crystal structure of DEN4 ED3 mutant with L387I

5B1C · Envelope protein E: “Crystal structure of DEN4 ED3 mutant with L387I”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.67). MolNFT v1 #114076 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B1C
Type: protein
Length: 296 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope protein E
UniProt: P09866
Ligands: SO4
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 2% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Envelope protein E	protein	97	3% helix, 48% strand	P09866
A	Envelope protein E	protein	101	0% helix, 49% strand	P09866
C	Envelope protein E	protein	98	3% helix, 48% strand	P09866

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains B, A, C

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

Pockets

3 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	469	0.67	0.78	35	SO4
2	96	0.62	0.89	23	empty
3	79	0.40	0.78	16	empty

Interfaces

3 interfaces between chains.

A–C · 700 Å² buried · 9 hydrogen bonds · protein-protein
B–A · 530 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 454 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5B1C · Crystal structure of DEN4 ED3 mutant with L387I · the same entry in another collection · chain B against B, 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 P09866
Elsewhere: RCSB PDB 5B1C · PDBe 5B1C · UniProt P09866

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