MolNFT v1 · #187098 · protein

Crystal structure of Fab in complex with mouse CD96 dimer

7S13 · Fab heavy chain: “Crystal structure of Fab in complex with mouse CD96 dimer”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.70). MolNFT v1 #187098 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7S13
Type: protein
Length: 1,065 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain; T-cell surface protein tactile
UniProt: Q3U0X8
Ligands: NAG
Pockets: 7 · best druggability 0.70

Structure

x-ray diffraction · 6 distinct chains · 6% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab heavy chain	protein	209	7% helix, 51% strand	—
L	Fab light chain	protein	209	5% helix, 55% strand	—
I	Fab heavy chain	protein	208	6% helix, 52% strand	—
M	Fab light chain	protein	208	6% helix, 54% strand	—
C	T-cell surface protein tactile	protein	117	5% helix, 58% strand	Q3U0X8
D	T-cell surface protein tactile	protein	114	3% helix, 58% strand	Q3U0X8

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, D
EDO · 1,2-ethanediol · additive · 3 copies · chains H, L, C
FLC · Citrate anion · additive · chains I

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

Pockets

7 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	830	0.70	0.76	69	empty
2	353	0.63	0.79	41	empty
3	467	0.58	0.73	54	empty
4	333	0.52	0.73	44	empty
5	96	0.41	0.77	19	empty

Interfaces

11 interfaces between chains.

H–L · 1727 Å² buried · 17 hydrogen bonds · protein-protein
I–M · 1693 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 916 Å² buried · 5 hydrogen bonds · protein-protein
I–C · 570 Å² buried · 12 hydrogen bonds · protein-protein
H–D · 565 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, cyclization).

Compared structures

7S13 · Crystal structure of Fab in complex with mouse CD96 dimer · the same entry in another collection · chain D against D, TM-score 1.00
Q3U0X8 · AlphaFold monomer V2.0 prediction for T-cell surface protein tactile (Q3U0X8) · a predicted model of the same protein · chain D against A, TM-score 0.89

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 Q3U0X8
Elsewhere: RCSB PDB 7S13 · PDBe 7S13 · UniProt Q3U0X8

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