MolNFT v1 · #5199 · protein

Catalytic domain of prommp-2 E404Q mutant

1EAK · 72 kda type IV collagenase: “Catalytic domain of prommp-2 E404Q mutant”. X-ray diffraction, 3 ligands (ZN, CA, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #5199 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1EAK
Type: protein
Length: 1,693 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 72 kda type IV collagenase; Inhibitor peptide
EC: 3.4.24.24
UniProt: P08253
Ligands: ZN, CA, SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	72 kda type IV collagenase (EC 3.4.24.24)	protein	421	19% helix, 18% strand	P08253
B, D	72 kda type IV collagenase (EC 3.4.24.24)	protein	419	20% helix, 19% strand	P08253
C	72 kda type IV collagenase (EC 3.4.24.24)	protein	418	17% helix, 17% strand	P08253
P, R	Inhibitor peptide	protein	8	0% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
CA · Calcium ion · metal · 8 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D, R, P

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1104	0.82	0.83	100	SO4
2	1035	0.82	0.83	90	SO4
3	857	0.77	0.81	68	empty
4	496	0.75	0.83	56	empty
5	340	0.68	0.81	42	empty

Interfaces

7 interfaces between chains.

B–D · 1025 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1002 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 613 Å² buried · 1 hydrogen bond · protein-protein
A–P · 512 Å² buried · 8 hydrogen bonds · protein-protein
D–R · 492 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide (disulfide).

Compared structures

1EAK · Catalytic domain of proMMP-2 E404Q mutant · the same entry in another collection · chain R against R, TM-score 1.00
P08253 · AlphaFold monomer V2.0 prediction for 72 kda type IV collagenase (P08253) · a predicted model of the same protein · chain B 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 P08253
Elsewhere: RCSB PDB 1EAK · PDBe 1EAK · UniProt P08253

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