MolNFT v1 · #120180 · protein

Crystal structure of homo-specific diabody

5GS1 · Light chain: “Crystal structure of homo-specific diabody”. X-ray diffraction, 20 pockets (best druggability 0.73). MolNFT v1 #120180 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GS1
Type: protein
Length: 3,175 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain; Heavy chain; Diabody
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 5 distinct chains · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, M, O, Q	Light chain	protein	106	6% helix, 46% strand	—
B, N, P, R	Heavy chain	protein	118	10% helix, 53% strand	—
C, D, E, F, I, J, K, L	Diabody	protein	229	9% helix, 48% strand	—
G	Diabody	protein	223	5% helix, 49% strand	—
H	Diabody	protein	224	5% helix, 49% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	625	0.73	0.80	63	empty
2	611	0.72	0.79	64	empty
3	789	0.72	0.77	99	empty
4	991	0.70	0.75	89	empty
5	887	0.67	0.74	77	empty

Interfaces

37 interfaces between chains.

I–J · 2099 Å² buried · 31 hydrogen bonds · protein-protein
K–L · 2093 Å² buried · 29 hydrogen bonds · protein-protein
G–H · 2084 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 2053 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 2026 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide (disulfide).

Compared structures

5GS1 · Crystal structure of homo-specific diabody · 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 5GS1 · PDBe 5GS1

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