MolNFT v1 · #126799 · protein

Structure of the family B DNA polymerase from the hyperthermophilic archaeon pyrobaculum calidifontis

5MDN: “Structure of the family B DNA polymerase from the hyperthermophilic archaeon pyrobaculum calidifontis”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.77). MolNFT v1 #126799 on GenesisL1: 3D structure, binding…

PDB: 5MDN
Type: protein
Length: 1,522 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase
EC: 2.7.7.7
UniProt: A3MV07
Ligands: MG
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA polymerase (EC 2.7.7.7)	protein	761	38% helix, 23% strand	A3MV07

Ligands and binding sites

MG · Magnesium ion · metal · 6 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	937	0.77	0.79	54	empty
2	1165	0.76	0.79	100	MG
3	927	0.74	0.77	57	MG
4	823	0.73	0.78	57	empty
5	364	0.68	0.81	36	empty

Interfaces

1 interface between chains.

A–B · 540 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5MDN · Structure of the family B DNA polymerase from the hyperthermophilic archaeon Pyrobaculum… · the same entry in another collection · chain A against A, 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 A3MV07
Elsewhere: RCSB PDB 5MDN · PDBe 5MDN · UniProt A3MV07

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