SMTL ID : 4itc.1

Crystal Structure Analysis of the K1 Cleaved Adhesin domain of Lys-gingipain (Kgp) from Porphyromonas gingivalis W83

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.20, D.22, D.24, H.26, N.62 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.20, A:D.22, A:D.24, A:H.26, H2O.1 CA.2: 6 residues within 4Å: Chain A: S.7, E.9, S.41, G.43, D.165, E.166 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.7, A:E.9, A:S.41, A:G.43, A:E.166

3 x GAI: GUANIDINE(Non-covalent)

GAI.3: 3 residues within 4Å: Chain A: P.72, N.73, A.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.73 GAI.4: 3 residues within 4Å: Chain A: Y.88, D.158, M.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.158, A:D.158 Salt bridges: A:D.158 GAI.6: 6 residues within 4Å: Chain A: I.12, P.13, A.14, W.16, K.17, T.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.12, A:W.16, A:T.18, A:T.18

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: S.15 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.15, A:S.15 GOL.7: 5 residues within 4Å: Chain A: L.4, S.5, E.6, W.16 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.5, A:S.5, A:W.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ganuelas, L.A. et al., The lysine gingipain adhesin domains from Porphyromonas gingivalis interact with erythrocytes and albumin: Structures correlate to function. Eur J Microbiol Immunol (Bp) (2013)

Release Date

2013-09-25

Peptides

Lys-gingipain W83: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lys-gingipain W83