MolNFT v1 · #4114 · protein

Crystal structure of human plasminogen catalytic domain

1DDJ: “Crystal structure of human plasminogen catalytic domain”. X-ray diffraction, 6 pockets (best druggability 0.59). MolNFT v1 #4114 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1DDJ
Type: protein
Length: 988 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasminogen
EC: 3.4.21.7
UniProt: P00747
Pockets: 6 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Plasminogen (EC 3.4.21.7)	protein	247	11% helix, 33% strand	P00747

Pockets

6 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	124	0.59	0.85	25	empty
2	118	0.53	0.82	23	empty
3	110	0.44	0.79	22	empty
4	116	0.44	0.78	22	empty
5	64	0.32	0.76	16	empty

Interfaces

2 interfaces between chains.

A–B · 563 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 559 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

1DDJ · Crystal structure of human plasminogen catalytic domain · the same entry in another collection · chain A against A, TM-score 1.00
P00747 · AlphaFold monomer V2.0 prediction for plasminogen (P00747) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P00747
Elsewhere: RCSB PDB 1DDJ · PDBe 1DDJ · UniProt P00747

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