SMTL ID : 4rf8.2 (1 other biounit)

Crystal structure of double-domain arginine kinase from Anthopleura japonicas in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

11 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 5 residues within 4Å: Chain A: T.459, G.693, L.694, Q.698 Ligands: NO3.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.459, A:G.693, A:Q.698 NO3.3: 4 residues within 4Å: Chain A: D.613, F.618, Y.626 Ligands: NO3.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.613, A:F.618 NO3.4: 5 residues within 4Å: Chain A: D.461, K.466, S.695, Q.698 Ligands: NO3.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.461, A:S.695 NO3.5: 6 residues within 4Å: Chain A: H.449, S.450, P.451, R.690, R.691, L.692 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.449, A:R.690, A:R.690, A:R.691, A:L.692 NO3.6: 3 residues within 4Å: Chain A: T.459, S.460, K.466 No protein-ligand interaction detected (PLIP) NO3.7: 6 residues within 4Å: Chain A: S.460, D.461, M.462, D.613, Y.626 Ligands: NO3.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.462, A:Y.626, A:Y.626 NO3.8: 4 residues within 4Å: Chain A: E.94, K.101, L.102, A.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.94, A:L.102, A:A.103 Water bridges: A:E.94 NO3.9: 6 residues within 4Å: Chain A: R.125, I.407, P.497, G.498, A.557, K.561 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.561 Water bridges: A:R.125, A:R.125, A:D.411 NO3.10: 4 residues within 4Å: Chain A: N.124, Y.126, R.128, K.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.128 NO3.11: 5 residues within 4Å: Chain A: L.153, E.156, S.178, E.213, G.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.178, A:G.214 Water bridges: A:S.178, A:R.215 NO3.12: 5 residues within 4Å: Chain A: S.70, G.71, V.72, G.73, Y.75 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.71, A:V.72, A:G.73, A:Y.75 Water bridges: A:S.70

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 9 residues within 4Å: Chain A: S.129, T.130, R.131, R.133, R.287, S.289, V.290, H.291, D.333 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.129, A:R.287, A:S.289, A:H.291 Water bridges: A:R.131 Salt bridges: A:R.131, A:R.131, A:R.133, A:R.236, A:R.287, A:R.287 pi-Stacking: A:H.291

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.13: 6 residues within 4Å: Chain A: Y.452, N.456, R.690, G.693, Q.698, D.702 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.690, A:D.702 EPE.14: 8 residues within 4Å: Chain A: P.464, E.465, V.467, D.468, A.469, D.597, G.599, S.600 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.465, A:A.469, A:S.600 Water bridges: A:G.599

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-04-08

Peptides

Arginine kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Arginine kinase

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