MolNFT v1 · #176119 · protein

Crystal structure of D12 Fab-ATP complex

7DC7 · D12 Fab heavy chain: “Crystal structure of D12 Fab-ATP complex”. X-ray diffraction, 1 ligand (ATP), 5 pockets (best druggability 0.53). MolNFT v1 #176119 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DC7
Type: protein
Length: 435 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D12 Fab heavy chain; D12 Fab light chain
Ligands: ATP
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D12 Fab heavy chain	protein	222	9% helix, 50% strand	—
B	D12 Fab light chain	protein	213	7% helix, 50% strand	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	340	0.53	0.74	49	empty
2	119	0.47	0.79	30	empty
3	128	0.44	0.77	18	ATP
4	71	0.33	0.76	20	empty
5	83	0.31	0.72	19	empty

Interfaces

1 interface between chains.

A–B · 1770 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).

Compared structures

7DC7 · Crystal structure of D12 Fab-ATP complex · 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 7DC7 · PDBe 7DC7

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