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Crystal structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae (semet labeled), RIM1 (FORM2)

Analyse Crystal structure of mitochondrial single-stranded DNA binding proteins from S.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CQO
Type: protein
Length: 750 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-stranded DNA-binding protein RIM1, mitochondrial
UniProt: P32445
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 10% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	95	11% helix, 58% strand	P32445
B	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	94	10% helix, 60% strand	P32445
C	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	93	10% helix, 58% strand	P32445
D	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	99	10% helix, 57% strand	P32445
E	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	94	10% helix, 48% strand	P32445
F	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	95	9% helix, 55% strand	P32445
G	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	89	11% helix, 58% strand	P32445
H	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	91	11% helix, 51% strand	P32445

Pockets

6 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	957	0.81	0.82	117	empty
2	597	0.64	0.75	82	empty
3	201	0.54	0.79	26	empty
4	119	0.48	0.79	21	empty
5	196	0.45	0.74	36	empty

Interfaces

15 interfaces between chains.

B–F · 1353 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 1140 Å² buried · 32 hydrogen bonds · protein-protein
A–G · 1127 Å² buried · 26 hydrogen bonds · protein-protein
D–F · 469 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 433 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified (engineered).

Compared structures

6CQO · Crystal Structure of mitochondrial single-stranded DNA binding proteins from S.… · the same entry in another collection · chain H against H, TM-score 1.00
P32445 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein RIM1… · a predicted model of the same protein · chain H 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 P32445
Elsewhere: RCSB PDB 6CQO · PDBe 6CQO · UniProt P32445

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