SMTL ID : 4iuw.1

Crystal structure of PEPO from Lactobacillus rhamnosis HN001 (DR20)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.478, H.482, E.538, H.591 Ligands: CIT.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.478, A:H.482, A:E.538, A:E.538

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 12 residues within 4Å: Chain A: N.437, A.438, T.475, H.478, E.479, H.482, E.538, W.573, H.591, R.597 Ligands: ZN.1, NA.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.437, A:N.437, A:N.437, A:E.479 Water bridges: A:T.475, A:T.475, A:H.478, A:R.597 Salt bridges: A:H.478, A:H.478, A:H.482, A:H.591, A:H.591, A:R.597

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 1 residues within 4Å: Ligands: CIT.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.437

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: R.523, Q.603, Y.621, R.622, K.626 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.603 Water bridges: A:R.523, A:R.523, A:Y.621, A:Q.623, A:K.626, A:K.626 Salt bridges: A:R.523, A:R.622, A:K.626 SO4.5: 2 residues within 4Å: Chain A: S.306, W.307 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.307 Water bridges: A:Q.75, A:Q.75, A:Q.75, A:Q.75, A:T.308

11 x CO3: CARBONATE ION(Non-functional Binders)

CO3.6: 1 residues within 4Å: Chain A: N.499 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.499 Water bridges: A:N.499 CO3.7: 1 residues within 4Å: Chain A: T.98 No protein-ligand interaction detected (PLIP) CO3.8: 2 residues within 4Å: Chain A: D.153, A.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.154 Water bridges: A:D.153 CO3.9: 2 residues within 4Å: Chain A: R.87, G.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.87 CO3.10: 4 residues within 4Å: Chain A: R.581, T.584, V.585 Ligands: CO3.15 No protein-ligand interaction detected (PLIP) CO3.11: 4 residues within 4Å: Chain A: T.359, W.360, L.361, S.362 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.361 CO3.12: 1 residues within 4Å: Chain A: A.57 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.57 CO3.13: 3 residues within 4Å: Chain A: R.288, S.305, H.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.310 Water bridges: A:R.288, A:R.288, A:K.309 CO3.14: 3 residues within 4Å: Chain A: E.356, N.358, K.366 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.356 CO3.15: 2 residues within 4Å: Chain A: Q.588 Ligands: CO3.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.588 CO3.16: 3 residues within 4Å: Chain A: P.241, A.242, L.420 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.242 Water bridges: A:K.243, A:L.420

1 x OXD: OXALIC ACID(Non-covalent)

OXD.17: 1 residues within 4Å: Chain A: R.371 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.371, A:R.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anderson, B.F. et al., Crystal structure of PEPO from Lactobacillus rhamnosis HN001 (DR20). TO BE PUBLISHED

Release Date

2013-03-20

Peptides

Neutral endopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neutral endopeptidase