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Crystal structure of trans-3-hydroxy-L-proline dehydratase in complex with substrate - closed conformation

Analyse Crystal structure of trans-3-hydroxy-L-proline dehydratase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6R77
Type: protein
Length: 696 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proline racemase
UniProt: H3ZMH8
Ligands: HY3
Pockets: 18 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Proline racemase	protein	348	23% helix, 41% strand	H3ZMH8

Ligands and binding sites

HY3 · 3-hydroxyproline · ligand · 2 copies · chains A, B

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

Pockets

18 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.72	0.98	21	empty
2	89	0.63	0.89	18	empty
3	98	0.62	0.87	15	empty
4	91	0.49	0.82	16	empty
5	79	0.48	0.82	16	empty

Interfaces

1 interface between chains.

A–B · 2947 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

6R77 · Crystal structure of trans-3-Hydroxy-L-proline dehydratase in complex with substrate… · the same entry in another collection · chain A against A, TM-score 1.00

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 H3ZMH8
Elsewhere: RCSB PDB 6R77 · PDBe 6R77 · UniProt H3ZMH8

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