MolNFT v1 · #141152 · protein

Crystal structure of the hyhl-hypa complex (form I)

5YXY · Cytosolic nife-hydrogenase, alpha subunit: “Crystal structure of the hyhl-hypa complex (form I)”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.74). MolNFT v1 #141152 on GenesisL1: 3D structure, binding sites and…

PDB: 5YXY
Type: protein
Length: 1,572 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytosolic nife-hydrogenase, alpha subunit; Probable hydrogenase nickel incorporation…
UniProt: Q8NKS2, Q5JIH3
Ligands: ZN
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 6 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytosolic nife-hydrogenase, alpha subunit	protein	404	44% helix, 17% strand	Q8NKS2
B	Cytosolic nife-hydrogenase, alpha subunit	protein	394	47% helix, 13% strand	Q8NKS2
C	Cytosolic nife-hydrogenase, alpha subunit	protein	406	46% helix, 16% strand	Q8NKS2
D	Probable hydrogenase nickel incorporation protein hypa	protein	124	30% helix, 31% strand	Q5JIH3
E	Probable hydrogenase nickel incorporation protein hypa	protein	123	29% helix, 32% strand	Q5JIH3
F	Probable hydrogenase nickel incorporation protein hypa	protein	121	31% helix, 31% strand	Q5JIH3

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	841	0.74	0.78	103	empty
2	76	0.70	0.95	19	empty
3	55	0.70	0.97	23	empty
4	280	0.69	0.84	52	empty
5	62	0.68	0.95	20	empty

Interfaces

15 interfaces between chains.

A–D · 839 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 763 Å² buried · 6 hydrogen bonds · protein-protein
C–F · 726 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 216 Å² buried · 1 hydrogen bond · protein-protein
A–B · 209 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5YXY · Crystal structure of the HyhL-HypA complex (form I) · the same entry in another collection · chain F against F, TM-score 1.00
Q5JIH3 · AlphaFold monomer V2.0 prediction for hydrogenase maturation factor hypa (Q5JIH3) · a predicted model of the same protein · chain F against A, TM-score 0.94

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 Q8NKS2
Every structure of UniProt Q5JIH3
Elsewhere: RCSB PDB 5YXY · PDBe 5YXY · UniProt Q8NKS2 · UniProt Q5JIH3

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