SMTL ID : 6pjw.4 (3 other biounits)

Adenylate kinase from Methanococcus igneus - AMP bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-trimer

Ligands

6 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 17 residues within 4Å: Chain A: P.12, N.38, F.39, G.40, M.43, R.56, M.59, R.60, Q.71, T.91, H.92, V.95, L.102, G.104, L.105, R.138 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.38, A:R.60, A:Q.71, A:T.91, A:G.104 Water bridges: A:G.40, A:G.40, A:R.56, A:M.59, A:R.138, A:R.138, A:R.138, A:R.140 Salt bridges: A:R.56, A:H.92, A:R.138 AMP.2: 15 residues within 4Å: Chain A: G.13, V.14, G.15, G.16, T.17, T.18, R.131, R.140, N.175, R.176, D.177, G.178, L.179, L.180 Ligands: MG.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.13, A:G.15, A:G.16, A:T.17, A:T.18, A:T.18, A:R.131, A:N.175, A:N.175, A:D.177, A:G.178, A:L.179 Water bridges: A:T.17, A:R.140, A:R.140 Salt bridges: A:R.140 pi-Cation interactions: A:R.131, A:R.131 AMP.4: 18 residues within 4Å: Chain B: N.38, F.39, G.40, M.43, R.56, D.57, M.59, R.60, Q.71, D.90, T.91, H.92, V.95, L.102, G.104, L.105, R.138, R.140 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.38, B:N.38, B:R.60, B:Q.71, B:T.91, B:G.104 Water bridges: B:R.138, B:R.138, B:R.138, B:R.138 Salt bridges: B:R.56, B:H.92, B:R.138 AMP.5: 16 residues within 4Å: Chain B: G.13, V.14, G.15, G.16, T.17, T.18, R.131, D.135, R.140, N.175, R.176, D.177, G.178, L.179, L.180 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.13, B:G.15, B:T.17, B:T.18, B:T.18, B:R.131, B:R.131, B:N.175, B:R.176, B:D.177, B:G.178 Water bridges: B:G.16, B:G.16, B:R.140 Salt bridges: B:R.140 pi-Cation interactions: B:R.131, B:R.131 AMP.7: 18 residues within 4Å: Chain C: P.12, N.38, F.39, G.40, M.43, R.56, M.59, R.60, Q.71, D.90, T.91, H.92, V.95, L.102, G.104, L.105, R.138 Ligands: MG.9 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:N.38, C:R.60, C:Q.71, C:T.91, C:G.104 Water bridges: C:T.17, C:D.90, C:R.138, C:R.138, C:R.138, C:R.138 Salt bridges: C:R.56, C:H.92, C:R.138 AMP.8: 16 residues within 4Å: Chain C: G.13, V.14, G.15, G.16, T.17, T.18, R.131, D.135, R.140, N.175, R.176, D.177, G.178, L.179, L.180 Ligands: MG.9 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.13, C:G.15, C:G.16, C:T.17, C:T.18, C:T.18, C:R.140, C:N.175, C:N.175, C:D.177 Water bridges: C:T.18 pi-Cation interactions: C:R.131, C:R.131

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: T.17, N.38, R.138, R.140 Ligands: AMP.1, AMP.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:T.17, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 6 residues within 4Å: Chain B: T.17, N.38, D.90, R.138, R.140 Ligands: AMP.5 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:T.17, H2O.1, H2O.1, H2O.1, H2O.2, H2O.2 MG.9: 4 residues within 4Å: Chain C: T.17, R.138 Ligands: AMP.7, AMP.8 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:T.17, H2O.2, H2O.2, H2O.2, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bae, E., Adenylate kinase from Methanococcus igneus - AMP bound form. To Be Published

Release Date

2020-01-22

Peptides

Adenylate kinase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
K

C
L

Adenylate kinase

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