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Crystal structure of vanx

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

PDB: 1R44
Type: protein
Length: 1,212 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-alanyl-D-alanine dipeptidase
EC: 3.4.13.-
UniProt: Q06241
Ligands: ZN
Pockets: 12 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	D-alanyl-D-alanine dipeptidase (EC 3.4.13.-)	protein	202	30% helix, 16% strand	Q06241

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	855	0.75	0.79	64	empty
2	765	0.72	0.78	67	ZN
3	711	0.72	0.78	69	ZN
4	454	0.63	0.76	55	empty
5	399	0.61	0.76	52	empty

Interfaces

5 interfaces between chains.

D–E · 947 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 943 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 585 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 554 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 462 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1R44 · Crystal Structure of VanX · the same entry in another collection · chain C against C, TM-score 1.00
Q06241 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine dipeptidase (Q06241) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q06241
Elsewhere: RCSB PDB 1R44 · PDBe 1R44 · UniProt Q06241

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