MolNFT v1 · #97279 · protein

Crystal structure of penicillin-binding protein 5 (PBP5) from pseudomonas aeruginosa in apo state

4K91 · D-ala-D-ala-carboxypeptidase: “Crystal structure of penicillin-binding protein 5 (PBP5) from pseudomonas aeruginosa in apo state”. X-ray diffraction, 3 pockets (best druggability 0.74). MolNFT v1 #97279 on GenesisL1: 3D structure…

PDB: 4K91
Type: protein
Length: 684 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-ala-D-ala-carboxypeptidase
EC: 3.4.16.4
UniProt: Q02SG6
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-ala-D-ala-carboxypeptidase (EC 3.4.16.4)	protein	342	30% helix, 31% strand	Q02SG6
B	D-ala-D-ala-carboxypeptidase (EC 3.4.16.4)	protein	342	31% helix, 34% strand	Q02SG6

Ligands and binding sites

SIN · Succinic acid · additive · 3 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	396	0.74	0.85	50	SIN
2	539	0.71	0.80	48	SIN
3	180	0.42	0.73	23	empty

Interfaces

1 interface between chains.

A–B · 631 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4K91 · Crystal structure of Penicillin-Binding Protein 5 (PBP5) from Pseudomonas aeruginosa in… · 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 Q02SG6
Elsewhere: RCSB PDB 4K91 · PDBe 4K91 · UniProt Q02SG6

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