SMTL ID : 1z83.2 (2 other biounits)

Crystal structure of human AK1A in complex with AP5A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-functional Binders)(Non-covalent)

ZN.1: 1 residues within 4Å: Ligands: AP5.6 No protein-ligand interaction detected (PLIP) ZN.2: 3 residues within 4Å: Chain A: E.71, E.105, R.109 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.71, A:E.105 ZN.3: 2 residues within 4Å: Chain A: E.27, H.37 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.27, A:H.37, H2O.5, H2O.5 ZN.7: 1 residues within 4Å: Ligands: AP5.10 No protein-ligand interaction detected (PLIP) ZN.8: 2 residues within 4Å: Chain B: E.27, H.37 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.27, B:H.37, H2O.9, H2O.10 ZN.9: 3 residues within 4Å: Chain B: E.71, D.75, R.109 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.71, B:D.75, B:D.75

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: T.36, K.84, T.87, S.88 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.84 SO4.5: 2 residues within 4Å: Chain A: S.1, M.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.2 Water bridges: A:S.1, A:E.3

2 x AP5: BIS(ADENOSINE)-5'-PENTAPHOSPHATE(Non-covalent)

AP5.6: 31 residues within 4Å: Chain A: G.17, P.18, G.19, S.20, G.21, K.22, G.23, T.24, T.40, G.41, L.44, R.45, M.62, Q.66, L.67, V.68, V.73, G.95, Y.96, R.98, Q.102, R.129, L.130, R.133, R.139, D.141, R.150, G.178, S.179, V.180 Ligands: ZN.1 51 PLIP interactions: 51 interactions with chain A Hydrogen bonds: A:G.19, A:S.20, A:G.21, A:K.22, A:G.23, A:T.24, A:T.24, A:T.40, A:Q.66, A:V.68, A:Q.102, A:Q.102, A:R.129, A:G.178 Water bridges: A:K.22, A:K.22, A:K.22, A:K.22, A:K.22, A:S.39, A:G.41, A:G.41, A:R.45, A:R.98, A:R.98, A:R.98, A:R.129, A:R.129, A:R.133, A:R.133, A:R.133, A:R.139, A:R.139, A:R.139, A:R.150, A:R.150, A:V.180 Salt bridges: A:K.22, A:K.22, A:K.22, A:R.45, A:R.133, A:R.133, A:R.139, A:R.139, A:R.139, A:R.150, A:R.150 pi-Cation interactions: A:R.98, A:R.129, A:R.129 AP5.10: 31 residues within 4Å: Chain B: G.17, P.18, G.19, S.20, G.21, K.22, G.23, T.24, T.40, G.41, L.44, R.45, M.62, Q.66, L.67, V.68, V.73, G.95, Y.96, R.98, Q.102, R.129, L.130, R.133, R.139, D.141, R.150, G.178, S.179, V.180 Ligands: ZN.7 45 PLIP interactions: 45 interactions with chain B Hydrogen bonds: B:G.19, B:S.20, B:G.21, B:K.22, B:G.23, B:T.24, B:T.24, B:T.40, B:G.41, B:Q.66, B:V.68, B:Q.102, B:Q.102, B:R.129, B:G.178 Water bridges: B:K.22, B:K.22, B:T.24, B:R.45, B:R.45, B:R.98, B:R.98, B:R.98, B:R.98, B:R.98, B:R.98, B:R.129, B:R.129, B:R.133, B:R.139, B:R.139, B:R.139 Salt bridges: B:K.22, B:K.22, B:K.22, B:R.45, B:R.133, B:R.133, B:R.139, B:R.139, B:R.139, B:R.150, B:R.150 pi-Cation interactions: B:R.98, B:R.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filippakopoulos, P. et al., Crystal structure of human AK1A in complex with AP5A. To be Published

Release Date

2005-04-26

Peptides

Adenylate kinase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Adenylate kinase 1

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