MolNFT v1 · #25204 · protein

Crystal structure of an hypothetical protein

1VIM · Hypothetical protein AF1796: “Crystal structure of an hypothetical protein”. X-ray diffraction, 12 pockets (best druggability 0.86). MolNFT v1 #25204 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VIM
Type: protein
Length: 760 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein AF1796
UniProt: O28478
Pockets: 12 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 55% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein AF1796	protein	192	55% helix, 11% strand	O28478
B	Hypothetical protein AF1796	protein	188	53% helix, 12% strand	O28478
C, D	Hypothetical protein AF1796	protein	190	56% helix, 12% strand	O28478

Ligands and binding sites

FMT · Formic acid · additive · 5 copies · chains A, C, B, D

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1200	0.86	0.87	130	FMT
2	75	0.77	0.99	19	empty
3	64	0.74	0.99	17	empty
4	352	0.69	0.82	50	FMT
5	345	0.69	0.82	45	FMT

Interfaces

6 interfaces between chains.

A–B · 2846 Å² buried · 40 hydrogen bonds · protein-protein
C–D · 2817 Å² buried · 42 hydrogen bonds · protein-protein
A–C · 1274 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 1257 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 169 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1VIM · Crystal structure of an hypothetical protein · the same entry in another collection · chain A against A, TM-score 1.00
O28478 · AlphaFold monomer V2.0 prediction for uncharacterized protein AF_1796 (O28478) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 O28478
Elsewhere: RCSB PDB 1VIM · PDBe 1VIM · UniProt O28478

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