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Crystal structure of the hypc-hypd-hype complex (form II)

Analyse Crystal structure of the hypc-hypd-hype complex (form II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VYU
Type: protein
Length: 726 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydrogenase EXPRESSION/FORMATION protein hypc; Hydrogenase EXPRESSION/FORMATION protein…
UniProt: Q5JII0, Q5JII1, Q5JII7
Ligands: SF4
Pockets: 5 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hydrogenase EXPRESSION/FORMATION protein hypc	protein	54	0% helix, 46% strand	Q5JII0
B	Hydrogenase EXPRESSION/FORMATION protein hypd	protein	367	43% helix, 17% strand	Q5JII1
C	Hydrogenase EXPRESSION/FORMATION protein hype	protein	305	31% helix, 26% strand	Q5JII7

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1127	0.85	0.86	108	empty
2	494	0.62	0.76	48	empty
3	163	0.46	0.75	18	empty
4	94	0.41	0.78	22	empty
5	93	0.38	0.76	22	empty

Interfaces

3 interfaces between chains.

B–C · 915 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 877 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 281 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3VYU · Crystal structure of the HypC-HypD-HypE complex (form II) · 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 Q5JII0
Every structure of UniProt Q5JII1
Every structure of UniProt Q5JII7
Elsewhere: RCSB PDB 3VYU · PDBe 3VYU · UniProt Q5JII0 · UniProt Q5JII1 · UniProt Q5JII7

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