SMTL ID : 3npf.1

Crystal structure of a putative dipeptidyl-peptidase VI (BACOVA_00612) from Bacteroides ovatus at 1.72 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 6 residues within 4Å: Chain A: N.22, R.24, F.29 Chain B: Y.171, L.172, W.173 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: Y.171, L.172, W.173 Chain B: N.22, R.24, F.29 Ligand excluded by PLIP

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: S.34, Y.60, W.173, A.174, D.182, S.184, R.200, D.201 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.60, A:D.182, A:S.184 Water bridges: A:Y.60, A:Y.60 GOL.3: 3 residues within 4Å: Chain A: I.160, E.161, R.223 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.223, A:R.223 Water bridges: A:Y.164, B:Q.104 GOL.4: 3 residues within 4Å: Chain A: G.209, Y.289, E.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.293, A:E.293 Water bridges: A:G.209 GOL.5: 7 residues within 4Å: Chain A: P.57, D.59, K.294, G.295, N.297, P.303, F.304 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.295 Water bridges: A:N.297, A:N.297, A:N.297 GOL.6: 5 residues within 4Å: Chain A: Q.2, M.7, Y.48, Y.52, R.66 No protein-ligand interaction detected (PLIP) GOL.8: 8 residues within 4Å: Chain B: S.34, Y.60, W.173, A.174, D.182, S.184, R.200, D.201 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.60, B:D.182, B:S.184 Water bridges: B:D.182, B:D.182, B:S.184 GOL.9: 2 residues within 4Å: Chain B: Y.60, T.61 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.59, B:Y.60, B:T.61 GOL.10: 2 residues within 4Å: Chain B: Y.207, E.239 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.207 GOL.11: 5 residues within 4Å: Chain B: I.214, A.215, P.216, F.218, L.280 No protein-ligand interaction detected (PLIP) GOL.12: 7 residues within 4Å: Chain B: S.151, L.152, K.153, T.162, M.193, H.194 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.153 Water bridges: B:T.162 GOL.13: 6 residues within 4Å: Chain B: T.89, H.91, T.162, S.165, M.193 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.162, B:S.165 Water bridges: B:T.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a putative dipeptidyl-peptidase VI (BACOVA_00612) from Bacteroides ovatus at 1.72 A resolution. To be published

Release Date

2010-07-28

Peptides

putative dipeptidyl-peptidase VI: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

putative dipeptidyl-peptidase VI