SMTL ID : 6n1c.1

Crystal structure of Inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: K.151, D.152, E.154, K.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.154, A:E.154, A:K.157 NA.2: 4 residues within 4Å: Chain A: F.53, T.55, E.154 Chain F: L.122 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:L.122 Water bridges: F:K.124 NA.8: 4 residues within 4Å: Chain D: D.79, D.111, A.112, K.113 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.79, D:K.113, D:K.113 Water bridges: D:S.72, D:D.79 NA.14: 4 residues within 4Å: Chain F: K.151, D.152, E.154, K.157 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.154, F:K.157, F:K.157

7 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 11 residues within 4Å: Chain A: F.59, P.61, H.138, S.142 Chain B: P.36, M.54, T.55, T.56, A.57 Chain D: P.85, M.125 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:P.36, B:A.57, A:F.59 Hydrogen bonds: A:H.138, A:S.142, A:S.142 MPD.6: 11 residues within 4Å: Chain A: P.36, M.54, T.55, T.56, A.57 Chain B: P.61, H.138, S.142 Chain F: P.85, V.86, M.125 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: B:S.142, B:S.142 Hydrophobic interactions: F:V.86, A:P.36 MPD.7: 10 residues within 4Å: Chain C: P.61, H.138, S.142 Chain E: P.85, V.86, M.125 Chain F: P.36, M.54, T.56, A.57 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: E:V.86, F:P.36 Hydrogen bonds: C:S.142, C:S.142 MPD.9: 13 residues within 4Å: Chain A: P.85, V.86, M.125 Chain D: F.59, P.61, H.138, L.139, S.142 Chain E: P.36, M.54, T.55, T.56, A.57 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: A:P.85, A:V.86, E:P.36, D:F.59 Hydrogen bonds: E:M.54, D:S.142 MPD.11: 7 residues within 4Å: Chain D: H.33, G.34, P.36, F.59 Chain E: H.33, G.34, F.59 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.59, E:F.59 Hydrogen bonds: E:H.33, E:G.34 MPD.12: 12 residues within 4Å: Chain C: P.85, V.86, M.125 Chain D: P.36, M.54, T.55, T.56, A.57 Chain E: F.59, P.61, H.138, S.142 6 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: E:F.59, C:V.86, D:P.36 Hydrogen bonds: E:H.138, E:S.142, E:S.142 MPD.13: 10 residues within 4Å: Chain B: P.85, V.86, M.125 Chain C: M.54, T.55, T.56 Chain F: F.59, P.61, H.138, S.142 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:F.59, B:P.85, B:V.86 Hydrogen bonds: F:S.142, F:S.142

2 x ALA: ALANINE(Non-covalent)

ALA.4: 4 residues within 4Å: Chain A: V.86, P.87 Chain D: V.86, P.87 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: A:P.87 Water bridges: A:H.33, B:E.35, D:H.33 Salt bridges: D:H.33 ALA.10: 4 residues within 4Å: Chain C: V.86, P.87 Chain E: V.86, P.87 6 PLIP interactions: 2 interactions with chain C, 1 interactions with chain F, 2 Ligand-Ligand interactions, 1 interactions with chain E Hydrophobic interactions: C:P.87 Water bridges: C:H.33, F:E.35 Hydrogen bonds: A.10, A.10 Salt bridges: E:H.33

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 8 residues within 4Å: Chain A: H.33, G.34, P.36, F.59 Chain B: H.33, G.34, P.36, F.59 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.59, A:F.59 Water bridges: B:H.33, A:H.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of Inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1. to be published

Release Date

2018-12-19

Peptides

Inorganic pyrophosphatase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Inorganic pyrophosphatase