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Structure of Viperin from Trichoderma virens

Analyse Structure of Viperin from Trichoderma virens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B4C
Type: protein
Length: 3,107 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.795
Source: Hypocrea virens (strain Gv29-8 / FGSC 10586)
Molecule: Viperin
UniProt: G9MQB8
Ligands: SO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · resolution 2.795 · 12 distinct chains · 36% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Viperin	protein	259	35% helix, 18% strand	G9MQB8
B	Viperin	protein	260	35% helix, 18% strand	G9MQB8
C	Viperin	protein	260	37% helix, 18% strand	G9MQB8
D	Viperin	protein	261	35% helix, 18% strand	G9MQB8
E	Viperin	protein	256	37% helix, 18% strand	G9MQB8
F	Viperin	protein	260	35% helix, 18% strand	G9MQB8
G	Viperin	protein	259	37% helix, 18% strand	G9MQB8
H	Viperin	protein	259	38% helix, 19% strand	G9MQB8
I	Viperin	protein	257	36% helix, 18% strand	G9MQB8
J	Viperin	protein	258	38% helix, 19% strand	G9MQB8
K	Viperin	protein	260	37% helix, 17% strand	G9MQB8
L	Viperin	protein	258	33% helix, 18% strand	G9MQB8

Ligands and binding sites

SO4 · Sulfate ion · ion · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
FLC · Citrate anion · additive · 12 copies · chains A, G, B, J, C, D, K, E, H, F, L, I

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	890	0.81	0.83	104	empty
2	1158	0.80	0.82	128	empty
3	656	0.80	0.85	92	empty
4	378	0.76	0.86	59	empty
5	755	0.73	0.78	71	SO4

Interfaces

25 interfaces between chains.

A–C · 534 Å² buried · 5 hydrogen bonds · protein-protein
D–F · 526 Å² buried · 5 hydrogen bonds · protein-protein
E–F · 523 Å² buried · 6 hydrogen bonds · protein-protein
G–I · 521 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 521 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

6B4C · Structure of viperin from trichoderma virens · 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 G9MQB8
Elsewhere: RCSB PDB 6B4C · PDBe 6B4C · UniProt G9MQB8

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