MolNFT v1 · #88951 · protein

Crystal structure of small single-stranded DNA-binding protein from streptomyces coelicolor

4DAM · Single-stranded DNA-binding protein 1: “Crystal structure of small single-stranded DNA-binding protein from streptomyces coelicolor”. X-ray diffraction, 11 pockets (best druggability 0.78). MolNFT v1 #88951 on GenesisL1: 3D…

PDB: 4DAM
Type: protein
Length: 1,287 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-stranded DNA-binding protein 1
UniProt: Q9KYI9
Pockets: 11 · best druggability 0.78

Structure

x-ray diffraction · 11 distinct chains · 9% helix, 64% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Single-stranded DNA-binding protein 1	protein	113	9% helix, 66% strand	Q9KYI9
B	Single-stranded DNA-binding protein 1	protein	108	9% helix, 67% strand	Q9KYI9
C	Single-stranded DNA-binding protein 1	protein	100	10% helix, 63% strand	Q9KYI9
D	Single-stranded DNA-binding protein 1	protein	109	9% helix, 59% strand	Q9KYI9
E	Single-stranded DNA-binding protein 1	protein	112	9% helix, 60% strand	Q9KYI9
F, I	Single-stranded DNA-binding protein 1	protein	110	9% helix, 67% strand	Q9KYI9
G	Single-stranded DNA-binding protein 1	protein	98	10% helix, 64% strand	Q9KYI9
H	Single-stranded DNA-binding protein 1	protein	108	7% helix, 67% strand	Q9KYI9
J	Single-stranded DNA-binding protein 1	protein	108	9% helix, 57% strand	Q9KYI9
K	Single-stranded DNA-binding protein 1	protein	111	9% helix, 68% strand	Q9KYI9
L	Single-stranded DNA-binding protein 1	protein	100	10% helix, 64% strand	Q9KYI9

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	851	0.78	0.81	99	empty
2	856	0.78	0.81	93	empty
3	1019	0.77	0.79	103	empty
4	421	0.64	0.78	53	empty
5	498	0.59	0.74	47	empty

Interfaces

24 interfaces between chains.

E–H · 1234 Å² buried · 21 hydrogen bonds · protein-protein
J–K · 1219 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 1207 Å² buried · 21 hydrogen bonds · protein-protein
F–G · 1182 Å² buried · 19 hydrogen bonds · protein-protein
I–L · 1167 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4DAM · Crystal structure of small single-stranded DNA-binding protein from Streptomyces… · the same entry in another collection · chain L against L, 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 Q9KYI9
Elsewhere: RCSB PDB 4DAM · PDBe 4DAM · UniProt Q9KYI9

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