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Crystal structure of a domain of a replication factor a protein, from methanocaldococcus jannaschii. northeast structural genomics target MJR118E

Analyse Crystal structure of a domain of a replication factor a protein, from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DM3
Type: protein
Length: 294 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Replication factor a
UniProt: Q58559
Ligands: NA
Pockets: 1 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 63% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Replication factor a	protein	98	8% helix, 63% strand	Q58559

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	503	0.69	0.79	52	empty

Interfaces

2 interfaces between chains.

A–C · 687 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 530 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3DM3 · Crystal structure of a domain of a Replication factor A protein, from Methanocaldococcus… · the same entry in another collection · chain A against A, TM-score 1.00
Q58559 · AlphaFold monomer V2.0 prediction for replication factor a (Q58559) · a predicted model of the same protein · chain A 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 Q58559
Elsewhere: RCSB PDB 3DM3 · PDBe 3DM3 · UniProt Q58559

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