MolNFT v1 · #126600 · protein

Engineering the thermostability of nanobodies - NBD2

5M7Q · Nanobody NBD2: “Engineering the thermostability of nanobodies - NBD2”. X-ray diffraction, 3 ligands (MG, CL, SO4), 1 pocket (best druggability 0.44). MolNFT v1 #126600 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5M7Q
Type: protein
Length: 250 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nanobody NBD2
Ligands: MG, CL, SO4
Pockets: 1 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Nanobody NBD2	protein	119	8% helix, 50% strand	—
A	Nanobody NBD2	protein	131	5% helix, 46% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains B, A
CL · Chloride ion · ion · 7 copies · chains B, A
SO4 · Sulfate ion · ion · 2 copies · chains B, A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.44	0.75	24	empty

Interfaces

1 interface between chains.

B–A · 621 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5M7Q · Engineering the Thermostability of Nanobodies - NbD2 · 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
Elsewhere: RCSB PDB 5M7Q · PDBe 5M7Q

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