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Structure of the octameric penicillin-binding protein homologue from pyrococcus abyssi

Analyse Structure of the octameric penicillin-binding protein homologue from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QMI
Type: protein
Length: 3,573 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pbp related beta-lactamase
EC: 3.5.2.6
UniProt: Q9V2D6
Ligands: DO3, LU
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F, G, H	Pbp related beta-lactamase (EC 3.5.2.6)	protein	447	32% helix, 29% strand	Q9V2D6
C, D, E	Pbp related beta-lactamase (EC 3.5.2.6)	protein	446	32% helix, 29% strand	Q9V2D6

Ligands and binding sites

DO3 · 10-((2R)-2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane 1,4,7-triacetic acid · ligand · 4 copies · chains E, F, G, H
LU · Lutetium (III) ion · metal · 17 copies · chains A, E, F

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1004	0.81	0.82	93	empty
2	1179	0.79	0.81	91	empty
3	1129	0.79	0.81	89	empty
4	1152	0.79	0.80	95	empty
5	1164	0.78	0.80	83	empty

Interfaces

16 interfaces between chains.

A–E · 3150 Å² buried · 33 hydrogen bonds · protein-protein
B–H · 2987 Å² buried · 41 hydrogen bonds · protein-protein
C–G · 2945 Å² buried · 30 hydrogen bonds · protein-protein
D–F · 2878 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 919 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

2QMI · Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi · 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 Q9V2D6
Elsewhere: RCSB PDB 2QMI · PDBe 2QMI · UniProt Q9V2D6

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