MolNFT v1 · #186298 · protein

Crystal structure of NB_0 in complex with FAB_8D3

7R9D · Fab 8D3 light chain: “Crystal structure of NB_0 in complex with FAB_8D3”. X-ray diffraction, 7 pockets (best druggability 0.59). MolNFT v1 #186298 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7R9D
Type: protein
Length: 554 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 8D3 light chain; Nanobody N0; Fab 8D3 heavy chain
Pockets: 7 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab 8D3 light chain	protein	218	6% helix, 52% strand	—
N	Nanobody N0	protein	113	5% helix, 49% strand	—
H	Fab 8D3 heavy chain	protein	223	10% helix, 51% strand	—

Pockets

7 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	514	0.59	0.74	53	empty
2	212	0.58	0.80	29	empty
3	52	0.51	0.88	20	empty
4	123	0.39	0.74	22	empty
5	62	0.33	0.77	14	empty

Interfaces

3 interfaces between chains.

L–H · 1955 Å² buried · 23 hydrogen bonds · protein-protein
L–N · 584 Å² buried · 9 hydrogen bonds · protein-protein
N–H · 488 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7R9D · Crystal structure of Nb_0 in complex with Fab_8D3 · the same entry in another collection · chain L against L, 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 7R9D · PDBe 7R9D

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