MolNFT v1 · #114627 · protein

Engineered digoxigenin binder DIG5.1A

5BVB: “Engineered digoxigenin binder DIG5.1A”. X-ray diffraction, 1 ligand (DOG), 6 pockets (best druggability 0.89). MolNFT v1 #114627 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5BVB
Type: protein
Length: 513 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DIG5.1A
Ligands: DOG
Pockets: 6 · best druggability 0.89

Structure

x-ray diffraction · 3 distinct chains · 25% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	DIG5.1A	protein	130	26% helix, 41% strand	—
B	DIG5.1A	protein	126	24% helix, 43% strand	—
D	DIG5.1A	protein	127	24% helix, 41% strand	—

Ligands and binding sites

DOG · Digoxigenin · ligand · 4 copies · chains A, C, B, D

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	827	0.89	0.92	82	DOG
2	282	0.71	0.84	26	DOG
3	312	0.63	0.79	34	DOG
4	239	0.54	0.77	35	empty
5	78	0.41	0.79	22	empty

Interfaces

4 interfaces between chains.

A–B · 899 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 781 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 222 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 46 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5BVB · Engineered Digoxigenin binder DIG5.1a · 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 5BVB · PDBe 5BVB

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