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Crystal structure of Fab dx-2930 in complex with human plasma kallikrein at 2.4 ångström resolution

Analyse Crystal structure of Fab dx-2930 in complex with human plasma kallikrein at 2.4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OGX
Type: protein
Length: 664 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasma kallikrein; Dx-2930 heavy chain; Dx-2930 light chain
EC: 3.4.21.34
UniProt: P03952
Ligands: SO4
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Plasma kallikrein (EC 3.4.21.34)	protein	236	13% helix, 36% strand	P03952
H	Dx-2930 heavy chain	protein	216	7% helix, 52% strand	—
L	Dx-2930 light chain	protein	212	6% helix, 51% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A

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

Pockets

9 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	51	0.60	0.93	16	empty
2	190	0.54	0.79	25	empty
3	311	0.53	0.74	40	empty
4	151	0.51	0.79	24	empty
5	103	0.43	0.77	17	empty

Interfaces

3 interfaces between chains.

H–L · 1682 Å² buried · 17 hydrogen bonds · protein-protein
A–H · 1011 Å² buried · 14 hydrogen bonds · protein-protein
A–L · 336 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4OGX · Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.4 Angstrom… · the same entry in another collection · chain A against A, TM-score 1.00
P03952 · AlphaFold monomer V2.0 prediction for plasma kallikrein (P03952) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P03952
Elsewhere: RCSB PDB 4OGX · PDBe 4OGX · UniProt P03952

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