MolNFT v1 · #102275 · protein

Crystal structure of Fab dx-2930 in complex with human plasma kallikrein at 2.1 ångström resolution

4OGY: “Crystal structure of Fab dx-2930 in complex with human plasma kallikrein at 2.1 ångström resolution”. X-ray diffraction, 16 pockets (best druggability 0.74). MolNFT v1 #102275 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4OGY
Type: protein
Length: 1,321 residues
Chains: 6
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
Pockets: 16 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Plasma kallikrein (EC 3.4.21.34)	protein	239	14% helix, 35% strand	P03952
H	Dx-2930 heavy chain	protein	219	5% helix, 52% strand	—
L, N	Dx-2930 light chain	protein	212	6% helix, 51% strand	—
M	Dx-2930 heavy chain	protein	200	5% helix, 55% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 3 copies · chains A, H, L

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1020	0.74	0.77	68	empty
2	526	0.67	0.78	51	empty
3	56	0.61	0.92	19	empty
4	295	0.61	0.79	41	EDO
5	214	0.56	0.79	26	empty

Interfaces

9 interfaces between chains.

H–L · 1704 Å² buried · 20 hydrogen bonds · protein-protein
M–N · 1669 Å² buried · 19 hydrogen bonds · protein-protein
A–H · 1060 Å² buried · 16 hydrogen bonds · protein-protein
B–M · 649 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 442 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4OGY · Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom… · the same entry in another collection · chain H against H, 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 4OGY · PDBe 4OGY · UniProt P03952

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