MolNFT v1 · #142576 · protein

Crystal structures of the serine protease domain of murine plasma kallikrein with peptide inhibitor mupain-1-16

6A8O: “Crystal structures of the serine protease domain of murine plasma kallikrein with peptide inhibitor…”. X-ray diffraction, 2 ligands (MRZ, MAN), 7 pockets (best druggability 0.67). MolNFT v1 #142576 on GenesisL1: 3D structure…

PDB: 6A8O
Type: protein
Length: 482 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasma kallikrein; Peptide inhibitor,
EC: 3.4.21.34
UniProt: P26262
Ligands: MRZ, MAN
Pockets: 7 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Plasma kallikrein (EC 3.4.21.34)	protein	236	11% helix, 33% strand	P26262
P	Peptide inhibitor,	protein	10	0% helix, 0% strand	—

Ligands and binding sites

MRZ · piperidine-1-carboximidamide · ligand · chains B, P
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	509	0.67	0.78	55	empty
2	254	0.66	0.83	30	empty
3	61	0.44	0.83	19	empty
4	107	0.40	0.76	16	empty
5	68	0.39	0.80	16	empty

Interfaces

2 interfaces between chains.

A–B · 680 Å² buried · 3 hydrogen bonds · protein-protein
B–P · 565 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 2 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

6A8O · Crystal structures of the serine protease domain of murine plasma kallikrein with peptide… · the same entry in another collection · chain A against A, TM-score 1.00
P26262 · AlphaFold monomer V2.0 prediction for plasma kallikrein (P26262) · a predicted model of the same protein · chain A 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 P26262
Elsewhere: RCSB PDB 6A8O · PDBe 6A8O · UniProt P26262

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