SMTL ID : 2qmi.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

17 x LU: LUTETIUM (III) ION(Non-functional Binders)

LU.1: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.9: 1 residues within 4Å: Ligands: DO3.11 Ligand excluded by PLIP LU.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.12: 1 residues within 4Å: Ligands: DO3.15 Ligand excluded by PLIP LU.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.16: 1 residues within 4Å: Ligands: DO3.19 Ligand excluded by PLIP LU.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LU.20: 1 residues within 4Å: Ligands: DO3.21 Ligand excluded by PLIP

4 x DO3: 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID(Non-covalent)

DO3.11: 5 residues within 4Å: Chain E: L.80, D.81, H.102, Y.286 Ligands: LU.9 3 PLIP interactions: 3 interactions with chain E Water bridges: E:D.81 Salt bridges: E:D.81, E:H.102 DO3.15: 4 residues within 4Å: Chain F: D.81, H.102, Y.286 Ligands: LU.12 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Y.286 Water bridges: F:D.81, F:D.81 Salt bridges: F:H.102 pi-Cation interactions: F:H.102 DO3.19: 4 residues within 4Å: Chain G: L.80, D.81, H.102 Ligands: LU.16 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Y.286, G:Y.286 Salt bridges: G:D.81, G:H.102 DO3.21: 5 residues within 4Å: Chain H: L.80, D.81, H.102, Y.286 Ligands: LU.20 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:L.80 Water bridges: H:D.81 Salt bridges: H:K.266 pi-Cation interactions: H:H.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delfosse, V. et al., Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family. Plos One (2009)

Release Date

2008-07-22

Peptides

Pbp related beta-lactamase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Pbp related beta-lactamase