MolNFT v1 · #97759 · protein

Crystal structure of WHY1 from arabidopsis thaliana

4KOO · Single-stranded DNA-binding protein WHY1, chloroplastic: “Crystal structure of WHY1 from arabidopsis thaliana”. X-ray diffraction, 2 ligands (NI, PO4), 9 pockets (best druggability 0.60). MolNFT v1 #97759 on GenesisL1: 3D structure…

PDB: 4KOO
Type: protein
Length: 678 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-stranded DNA-binding protein WHY1, chloroplastic
UniProt: Q9M9S3
Ligands: NI, PO4
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Single-stranded DNA-binding protein WHY1, chloroplastic	protein	176	22% helix, 40% strand	Q9M9S3
B	Single-stranded DNA-binding protein WHY1, chloroplastic	protein	162	20% helix, 43% strand	Q9M9S3
C	Single-stranded DNA-binding protein WHY1, chloroplastic	protein	165	19% helix, 43% strand	Q9M9S3
D	Single-stranded DNA-binding protein WHY1, chloroplastic	protein	175	25% helix, 41% strand	Q9M9S3

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A
PO4 · Phosphate ion · ion · chains B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 6 copies · chains A, B, C, D

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

Pockets

9 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	403	0.60	0.76	53	empty
2	271	0.53	0.75	42	empty
3	295	0.52	0.74	35	empty
4	136	0.48	0.79	24	empty
5	122	0.41	0.75	21	empty

Interfaces

5 interfaces between chains.

C–D · 1591 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1208 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 245 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 226 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 183 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4KOO · Crystal Structure of WHY1 from Arabidopsis thaliana · the same entry in another collection · chain D against D, TM-score 1.00
Q9M9S3 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein WHY1… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q9M9S3
Elsewhere: RCSB PDB 4KOO · PDBe 4KOO · UniProt Q9M9S3

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