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Crystal structure of hypa

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

PDB: 3A43
Type: protein
Length: 257 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydrogenase nickel incorporation protein hypa
UniProt: Q5JIH3
Ligands: ZN
Pockets: 4 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hydrogenase nickel incorporation protein hypa	protein	139	30% helix, 27% strand	Q5JIH3
B	Hydrogenase nickel incorporation protein hypa	protein	118	26% helix, 29% strand	Q5JIH3

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	132	0.46	0.77	26	empty
2	70	0.38	0.78	19	empty
3	51	0.38	0.80	14	empty
4	68	0.31	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 648 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (formylation).

Compared structures

3A43 · Crystal structure of HypA · the same entry in another collection · chain A against A, TM-score 1.00
Q5JIH3 · AlphaFold monomer V2.0 prediction for hydrogenase maturation factor hypa (Q5JIH3) · a predicted model of the same protein · chain B against A, TM-score 0.90

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 Q5JIH3
Elsewhere: RCSB PDB 3A43 · PDBe 3A43 · UniProt Q5JIH3

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