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Crystal structure of rhodostomin argdp mutant

Analyse Crystal structure of rhodostomin argdp mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4M4C
Type: protein
Length: 260 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Zinc METALLOPROTEINASE/DISINTEGRIN
EC: 3.4.24.-
UniProt: P30403
Ligands: SO4
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Zinc METALLOPROTEINASE/DISINTEGRIN (EC 3.4.24.-)	protein	65	0% helix, 23% strand	P30403

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains B, C, A, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	955	0.70	0.75	78	empty
2	165	0.45	0.75	37	empty

Interfaces

6 interfaces between chains.

C–D · 557 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 321 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 211 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 89 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 78 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

4M4C · Crystal structure of Rhodostomin ARGDP mutant · the same entry in another collection · chain A against A, TM-score 1.00
P30403 · AlphaFold monomer V2.0 prediction for zinc METALLOPROTEINASE/DISINTEGRIN (P30403) · a predicted model of the same protein · chain A against A, TM-score 0.86

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 P30403
Elsewhere: RCSB PDB 4M4C · PDBe 4M4C · UniProt P30403

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