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Crystal structure of the C-terminal domain of meca

Analyse Crystal structure of the C-terminal domain of meca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JTP
Type: protein
Length: 371 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adapter protein meca 1
UniProt: P37958
Ligands: IOD
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adapter protein meca 1	protein	92	40% helix, 29% strand	P37958
B, C, D	Adapter protein meca 1	protein	93	39% helix, 29% strand	P37958

Ligands and binding sites

IOD · Iodide ion · ion · 35 copies · chains A, B, C, D

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

Pockets

4 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	454	0.67	0.79	55	IOD
2	109	0.49	0.81	24	empty
3	215	0.47	0.74	23	IOD
4	82	0.47	0.82	23	IOD

Interfaces

5 interfaces between chains.

A–D · 578 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 550 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 434 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 371 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 196 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3JTP · crystal structure of the C-terminal domain of MecA · the same entry in another collection · chain A against A, TM-score 1.00
P37958 · AlphaFold monomer V2.0 prediction for adapter protein meca 1 (P37958) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P37958
Elsewhere: RCSB PDB 3JTP · PDBe 3JTP · UniProt P37958

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