SMTL ID : 3cpx.1

Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga hutchinsonii ATCC 33406 at 2.39 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-trimer

Ligands

6 x FE: FE (III) ION(Non-covalent)

FE.1: 7 residues within 4Å: Chain A: H.84, D.165, D.166, E.191, E.192, D.218 Ligands: FE.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.84, A:D.165, A:D.218, A:D.218, H2O.3 FE.2: 4 residues within 4Å: Chain A: D.165, E.192, H.296 Ligands: FE.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.165, A:E.192, A:E.192, A:H.296, H2O.3 FE.9: 4 residues within 4Å: Chain B: D.165, E.192, H.296 Ligands: FE.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.165, B:E.192, B:E.192, B:H.296, H2O.6 FE.10: 6 residues within 4Å: Chain B: H.84, D.165, E.191, E.192, D.218 Ligands: FE.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.84, B:D.165, B:D.218, H2O.6, H2O.6 FE.13: 4 residues within 4Å: Chain C: D.165, E.192, H.296 Ligands: FE.14 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.165, C:E.192, C:E.192, C:H.296 FE.14: 7 residues within 4Å: Chain C: H.84, D.165, D.166, E.191, E.192, D.218 Ligands: FE.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.84, C:D.165, C:D.218, C:D.218, H2O.11

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: Y.61, D.63, D.65, L.66, W.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.65 EDO.4: 4 residues within 4Å: Chain A: R.239, M.240, R.274 Chain B: G.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.274 EDO.5: 7 residues within 4Å: Chain A: T.220, W.221, D.238, E.264, G.269, A.270, F.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.220, A:E.264, A:A.270 EDO.6: 5 residues within 4Å: Chain A: G.194, S.271, R.274, E.275 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.194, A:S.271 Water bridges: A:E.275 EDO.7: 4 residues within 4Å: Chain A: A.199, E.275 Chain C: L.278 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: R.243, K.245, Y.246, R.249, D.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.249 Water bridges: A:R.243 EDO.12: 7 residues within 4Å: Chain A: Y.206, P.282 Chain B: D.65, L.66, Y.200, R.203, W.204 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.206, B:R.203, B:R.203 EDO.15: 7 residues within 4Å: Chain C: T.220, W.221, D.238, E.264, G.269, A.270, F.287 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.220, C:G.269 EDO.16: 8 residues within 4Å: Chain B: Y.206, P.282 Chain C: D.65, L.66, Y.200, R.203, W.204 Ligands: EDO.18 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.206, C:R.203, C:R.203 EDO.17: 4 residues within 4Å: Chain A: H.193, G.194 Chain C: R.239, M.240 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Water bridges: A:G.102, A:G.102, A:E.192, A:H.193 Hydrogen bonds: C:R.239 EDO.18: 6 residues within 4Å: Chain C: Y.61, D.63, D.65, L.66, W.204 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.65 EDO.19: 4 residues within 4Å: Chain C: R.239, A.268, G.269, A.270 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.239, C:G.269

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

CL.11: 3 residues within 4Å: Chain B: T.220, D.238, F.287 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga hutchinsonii ATCC 33406 at 2.39 A resolution. To be published

Release Date

2008-04-29

Peptides

Aminopeptidase, M42 family: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Aminopeptidase, M42 family