SMTL ID : 4br2.1

rat NTPDase2 in complex with Ca UMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x UNP: 5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]uridine(Non-covalent)

UNP.1: 21 residues within 4Å: Chain A: G.42, S.43, S.44, H.45, T.117, A.118, G.119, E.160, L.197, G.198, G.199, A.200, S.201, R.240, D.241, S.341, A.342, Y.345, R.389 Ligands: CA.2, GOL.6 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:S.43, A:S.44, A:S.44, A:S.44, A:H.45, A:H.45, A:T.117, A:T.117, A:A.118, A:G.119, A:G.199, A:A.200, A:S.201, A:R.240, A:R.389 Water bridges: A:G.198, A:Q.203, A:S.341, A:Y.393, A:Y.393, A:Y.393 Salt bridges: A:H.45 pi-Stacking: A:Y.345 pi-Cation interactions: A:R.389

1 x CA: CALCIUM ION(Non-functional Binders)

CA.2: 1 residues within 4Å: Ligands: UNP.1 No protein-ligand interaction detected (PLIP)

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: L.244, L.245, L.248, W.261, D.392 Ligands: GOL.6, GOL.7, GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.392 Water bridges: A:L.245, A:H.258 GOL.4: 7 residues within 4Å: Chain A: F.163, V.166, L.223, G.434, L.437, N.438, I.443 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.434, A:N.438 Water bridges: A:L.437, A:I.443 GOL.5: 7 residues within 4Å: Chain A: K.34, Y.35, W.53, S.109, P.111, R.150, T.440 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.34, A:Y.35 Water bridges: A:S.109, A:S.109, A:S.109, A:R.150, A:R.150 GOL.6: 7 residues within 4Å: Chain A: R.240, D.241, L.244, R.389, D.392 Ligands: UNP.1, GOL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.240, A:R.240, A:D.241, A:R.389 Water bridges: A:D.241 GOL.7: 8 residues within 4Å: Chain A: Y.265, W.376, K.387, R.389, L.390, A.391, D.392 Ligands: GOL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.389, A:L.390, A:A.391, A:D.392 Water bridges: A:Y.265 GOL.8: 6 residues within 4Å: Chain A: L.245, Q.268, V.269, L.270, E.273 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.270, A:L.270, A:E.273 GOL.9: 5 residues within 4Å: Chain A: Y.344, V.347, D.348, T.351, F.420 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.351, A:T.352, A:F.420 Water bridges: A:F.420

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zebisch, M. et al., Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases. Structure (2013)

Release Date

2013-07-17

Peptides

ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2

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