MolNFT v1 · #144085 · protein

Sirpalpha antibody complex

6BIT · KWAR23 Fab heavy chain: “Sirpalpha antibody complex”. X-ray diffraction, 16 pockets (best druggability 0.74). MolNFT v1 #144085 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6BIT
Type: protein
Length: 1,073 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: KWAR23 Fab heavy chain; KWAR23 Fab light chain; Tyrosine-protein phosphatase non-receptor…
UniProt: P78324
Pockets: 16 · best druggability 0.74

Structure

x-ray diffraction · 6 distinct chains · 5% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	KWAR23 Fab heavy chain	protein	213	7% helix, 53% strand	—
K	KWAR23 Fab light chain	protein	212	7% helix, 54% strand	—
H	Tyrosine-protein phosphatase non-receptor type substrate 1	protein	115	3% helix, 43% strand	P78324
J	KWAR23 Fab heavy chain	protein	207	4% helix, 53% strand	—
L	KWAR23 Fab light chain	protein	211	6% helix, 51% strand	—
G	Tyrosine-protein phosphatase non-receptor type substrate 1	protein	115	3% helix, 43% strand	P78324

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	474	0.74	0.83	63	empty
2	171	0.69	0.88	26	empty
3	260	0.64	0.81	42	empty
4	131	0.59	0.84	21	empty
5	92	0.59	0.87	19	empty

Interfaces

10 interfaces between chains.

J–L · 1630 Å² buried · 18 hydrogen bonds · protein-protein
I–K · 1606 Å² buried · 15 hydrogen bonds · protein-protein
J–G · 604 Å² buried · 17 hydrogen bonds · protein-protein
I–H · 559 Å² buried · 14 hydrogen bonds · protein-protein
K–L · 484 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 10 disulfide, 2 modified (disulfide, cyclization).

Compared structures

6BIT · SIRPalpha antibody complex · the same entry in another collection · chain G against G, TM-score 1.00
P78324 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type… · a predicted model of the same protein · chain H against A, TM-score 0.97

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 P78324
Elsewhere: RCSB PDB 6BIT · PDBe 6BIT · UniProt P78324

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