SMTL ID : 4bvp.1

Legionella pneumophila NTPDase1 crystal form II (closed) in complex with heptamolybdate and octamolybdate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: E.200, H.203 Chain B: E.200, H.203 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.203, B:E.200

2 x MOO: MOLYBDATE ION(Non-covalent)

MOO.2: 11 residues within 4Å: Chain A: G.18, S.19, T.85, A.86, G.87, E.126, G.155, G.156, A.157, S.158 Ligands: MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.19, A:T.85, A:T.85, A:A.86, A:G.87, A:G.156, A:A.157, A:S.158 Water bridges: A:T.85, A:G.155, A:Q.160 MOO.20: 11 residues within 4Å: Chain B: G.18, S.19, T.85, A.86, G.87, E.126, G.155, G.156, A.157, S.158 Ligands: MG.21 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.19, B:T.85, B:T.85, B:A.86, B:G.87, B:G.156, B:A.157, B:S.158, B:S.158 Water bridges: B:T.20, B:T.85, B:E.126, B:E.126, B:E.126, B:G.155

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.126 Ligands: MOO.2 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: Q.274 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: E.200 Chain B: E.200 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain B: E.126 Ligands: MOO.20 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Chain B: Q.274 No protein-ligand interaction detected (PLIP)

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 8 residues within 4Å: Chain A: H.191, F.193, V.242, H.243, K.244, Q.248 Chain B: N.207, E.234 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:N.207, B:S.208, A:L.194 Salt bridges: B:E.234, A:H.191, A:H.243 Hydrogen bonds: A:Q.248 MES.22: 9 residues within 4Å: Chain A: N.207, S.208, E.234 Chain B: H.191, F.193, V.242, H.243, K.244, Q.248 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.248 Water bridges: B:L.194, A:S.208 Salt bridges: B:H.191, B:H.243, A:E.234

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: Q.198, T.199, Y.313, Q.316 Chain B: P.92 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.198, A:S.202, A:Q.316, A:Q.316 Water bridges: A:Y.313, A:Y.313 GOL.12: 6 residues within 4Å: Chain A: N.124, D.125, L.128, H.174, V.177 Ligands: 6LL.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.124, A:D.125, A:H.174 GOL.24: 6 residues within 4Å: Chain A: P.92 Chain B: Q.198, T.199, S.202, Y.313, Q.316 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.198, B:T.199, B:S.202, B:Q.316 GOL.26: 4 residues within 4Å: Chain B: S.272, D.310, D.311 Ligands: M27.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.272 GOL.28: 5 residues within 4Å: Chain B: Q.109, Q.110, S.111, Q.112 Ligands: M27.27 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.110, B:S.111, B:Q.112 GOL.30: 6 residues within 4Å: Chain B: N.124, D.125, L.128, H.174, V.177 Ligands: 6LL.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.174 Water bridges: B:N.124 GOL.33: 6 residues within 4Å: Chain B: D.16, G.18, T.20, G.21, R.23, K.47 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.16, B:G.18, B:T.20, B:T.20, B:R.23 Water bridges: B:T.20, B:G.21

4 x M27: bis(mu2-oxo)-octaoxo-dimolybdenum (VI)(Non-covalent)

M27.7: 6 residues within 4Å: Chain A: S.273, Q.274, Y.308, D.310, D.311 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.274, A:Q.274 Water bridges: A:D.310 M27.9: 8 residues within 4Å: Chain A: A.71, H.76, W.106, Q.110, S.111, Q.112, W.113 Ligands: EDO.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.71, A:H.76, A:Q.110, A:S.111, A:Q.112, A:Q.112, A:W.113 M27.25: 6 residues within 4Å: Chain B: S.273, Q.274, Y.308, D.310, D.311 Ligands: GOL.26 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.274, B:Q.274 Water bridges: B:D.310, B:D.310 M27.27: 9 residues within 4Å: Chain B: L.70, A.71, H.76, W.106, Q.110, S.111, Q.112, W.113 Ligands: GOL.28 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.70, B:A.71, B:H.76, B:S.111, B:Q.112, B:W.113

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

EDO.8: 3 residues within 4Å: Chain A: D.310, D.311 Ligands: M27.7 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain A: Q.110, S.111 Ligands: M27.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.110, A:S.111, A:Q.112 EDO.13: 5 residues within 4Å: Chain A: Y.83, K.119, I.121, D.125 Ligands: 6LL.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.119, A:D.125 EDO.31: 5 residues within 4Å: Chain B: Y.83, K.119, I.121, D.125 Ligands: 6LL.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.119, B:K.119, B:D.125

2 x 6LL: TETRAKIS-(MU-OXO)-DECA-OXO-TRIMOLYBDENUM(Non-covalent)

6LL.11: 9 residues within 4Å: Chain A: K.119, I.121, T.122, D.125, L.128, F.129, H.358 Ligands: GOL.12, EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.119, A:T.122 6LL.29: 9 residues within 4Å: Chain B: K.119, I.121, T.122, D.125, L.128, F.129, H.358 Ligands: GOL.30, EDO.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.119, B:T.122

2 x MO7: bis(mu4-oxo)-bis(mu3-oxo)-octakis(mu2-oxo)-dodecaoxo-heptamolybdenum (VI)(Non-covalent)

MO7.14: 7 residues within 4Å: Chain A: R.23, K.47, K.49, N.269, E.312, N.348 Ligands: 8M0.19 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.23, A:K.47, A:K.47, A:K.49, A:N.348 Water bridges: A:R.23, A:E.312 MO7.32: 7 residues within 4Å: Chain B: R.23, K.47, K.49, N.269, E.312, N.348 Ligands: 8M0.16 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.23, B:K.47, B:K.47, B:K.49, B:N.348 Water bridges: B:R.23, B:E.312

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

CL.15: 5 residues within 4Å: Chain A: N.207, P.219, D.220 Chain B: R.89, G.123 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain A: R.89, G.123 Chain B: N.207, P.219, D.220 Ligand excluded by PLIP

2 x 8M0: bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)(Covalent)(Non-covalent)

8M0.16: 8 residues within 4Å: Chain A: P.92, S.94, Q.95, K.98 Chain B: K.49, E.312, Y.313 Ligands: MO7.32 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.49, B:K.49, B:E.312, B:Y.313, A:S.94, A:Q.95, A:K.98, A:K.98 Water bridges: B:P.309, B:Y.313, A:S.94, A:S.94 8M0.19: 8 residues within 4Å: Chain A: K.49, E.312, Y.313 Chain B: P.92, S.94, Q.95, K.98 Ligands: MO7.14 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.49, A:K.49, A:E.312, B:S.94, B:Q.95, B:K.98, B:K.98 Water bridges: A:Y.313, B:S.94, B:S.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zebisch, M. et al., Structures of Legionella Pneumophila Ntpdase1 in Complex with Polyoxometallates. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-02-12

Peptides

ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

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