MolNFT v1 · #137352 · protein

The hapten triclocarban bound to the single domain camelid nanobody vhh T9

5VM0: “The hapten triclocarban bound to the single domain camelid nanobody vhh T9”. X-ray diffraction, 1 ligand (9EG), 3 pockets (best druggability 0.59). MolNFT v1 #137352 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VM0
Type: protein
Length: 252 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Camelid nanobody vhh T9
Ligands: 9EG
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Camelid nanobody vhh T9	protein	125	7% helix, 50% strand	—
B	Camelid nanobody vhh T9	protein	127	7% helix, 50% strand	—

Ligands and binding sites

9EG · N-(4-chlorophenyl)-N'-(3,4-dichlorophenyl)urea · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	81	0.59	0.88	23	9EG
2	90	0.58	0.87	25	9EG
3	222	0.51	0.76	35	EDO

Interfaces

1 interface between chains.

A–B · 273 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5VM0 · The hapten triclocarban bound to the single domain camelid nanobody VHH T9 · 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
Elsewhere: RCSB PDB 5VM0 · PDBe 5VM0

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