SMTL ID : 2ajp.3 (2 other biounits)

Crystal structure of a human pyridoxal kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.132, S.201 Ligands: ANP.22 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.132 MG.23: 4 residues within 4Å: Chain B: D.132, N.164, S.201 Ligands: ANP.44 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.132

40 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 4 residues within 4Å: Chain A: G.246, T.247, G.248 Ligands: ANP.22 Ligand excluded by PLIP UNX.3: 5 residues within 4Å: Chain A: R.20, E.48, D.50, Y.91 Chain B: R.30 Ligand excluded by PLIP UNX.4: 5 residues within 4Å: Chain A: T.96, G.97, C.126, D.127, Y.150 Ligand excluded by PLIP UNX.5: 6 residues within 4Å: Chain A: V.28, R.30, G.31, N.59, H.60, E.304 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Chain A: H.278, Q.282 Ligand excluded by PLIP UNX.7: 4 residues within 4Å: Chain A: Q.25, G.97, Y.98, D.249 Ligand excluded by PLIP UNX.8: 5 residues within 4Å: Chain A: N.35, R.36, T.39, F.40 Chain B: Q.43 Ligand excluded by PLIP UNX.9: 7 residues within 4Å: Chain A: N.89, K.90, Y.91, L.115, Q.118, N.119, L.122 Ligand excluded by PLIP UNX.10: 5 residues within 4Å: Chain A: P.156, L.157, A.158, G.193, P.194 Ligand excluded by PLIP UNX.11: 1 residues within 4Å: Chain A: Q.179 Ligand excluded by PLIP UNX.12: 5 residues within 4Å: Chain A: H.60, P.300, L.303, E.304 Ligands: UNX.13 Ligand excluded by PLIP UNX.13: 5 residues within 4Å: Chain A: Y.32, V.245, E.304, L.305 Ligands: UNX.12 Ligand excluded by PLIP UNX.14: 4 residues within 4Å: Chain A: H.262, P.263, N.264, N.265 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: L.213, K.239 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: F.47, H.260 Ligand excluded by PLIP UNX.17: 5 residues within 4Å: Chain A: D.127, T.162, T.200, G.248 Ligands: ANP.22 Ligand excluded by PLIP UNX.18: 5 residues within 4Å: Chain A: R.30, G.31, Y.32, R.36 Chain B: D.50 Ligand excluded by PLIP UNX.19: 6 residues within 4Å: Chain A: Q.43, F.47, I.49 Chain B: Y.32, R.36, V.308 Ligand excluded by PLIP UNX.20: 5 residues within 4Å: Chain A: V.308, K.311 Chain B: Q.43, V.44, G.46 Ligand excluded by PLIP UNX.21: 6 residues within 4Å: Chain A: H.27, V.28, I.29, R.36 Chain B: D.50, A.51 Ligand excluded by PLIP UNX.24: 5 residues within 4Å: Chain A: D.50 Chain B: R.30, G.31, Y.32, R.36 Ligand excluded by PLIP UNX.25: 7 residues within 4Å: Chain A: Y.32, R.36, V.308 Chain B: Q.43, F.47, E.48, I.49 Ligand excluded by PLIP UNX.26: 5 residues within 4Å: Chain A: Q.43, V.44, G.46 Chain B: V.308, K.311 Ligand excluded by PLIP UNX.27: 6 residues within 4Å: Chain A: D.50, A.51 Chain B: H.27, V.28, I.29, R.36 Ligand excluded by PLIP UNX.28: 5 residues within 4Å: Chain B: G.246, T.247, G.248, D.249 Ligands: ANP.44 Ligand excluded by PLIP UNX.29: 5 residues within 4Å: Chain A: R.30 Chain B: R.20, E.48, D.50, Y.91 Ligand excluded by PLIP UNX.30: 6 residues within 4Å: Chain B: T.96, G.97, Y.124, C.126, D.127, Y.150 Ligand excluded by PLIP UNX.31: 6 residues within 4Å: Chain B: V.28, R.30, G.31, N.59, H.60, E.304 Ligand excluded by PLIP UNX.32: 1 residues within 4Å: Chain B: H.278 Ligand excluded by PLIP UNX.33: 5 residues within 4Å: Chain B: Q.25, G.34, G.97, Y.98, D.249 Ligand excluded by PLIP UNX.34: 5 residues within 4Å: Chain A: Q.43 Chain B: N.35, R.36, T.39, F.40 Ligand excluded by PLIP UNX.35: 7 residues within 4Å: Chain B: N.89, K.90, Y.91, L.115, Q.118, N.119, L.122 Ligand excluded by PLIP UNX.36: 4 residues within 4Å: Chain B: P.156, L.157, A.158, D.159 Ligand excluded by PLIP UNX.37: 3 residues within 4Å: Chain B: S.178, Q.179, P.205 Ligand excluded by PLIP UNX.38: 5 residues within 4Å: Chain B: F.244, V.245, L.303, E.304 Ligands: UNX.39 Ligand excluded by PLIP UNX.39: 5 residues within 4Å: Chain B: Y.32, V.245, E.304, L.305 Ligands: UNX.38 Ligand excluded by PLIP UNX.40: 4 residues within 4Å: Chain B: H.262, P.263, N.264, N.265 Ligand excluded by PLIP UNX.41: 1 residues within 4Å: Chain B: L.213 Ligand excluded by PLIP UNX.42: 4 residues within 4Å: Chain B: L.45, F.47, H.260, K.261 Ligand excluded by PLIP UNX.43: 5 residues within 4Å: Chain B: D.127, T.162, T.200, G.248 Ligands: ANP.44 Ligand excluded by PLIP

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.22: 20 residues within 4Å: Chain A: D.127, V.129, D.132, N.164, E.167, T.200, S.201, L.213, V.215, V.240, A.242, F.244, T.247, G.248, F.251, L.277, L.281 Ligands: MG.1, UNX.2, UNX.17 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.164, A:T.200, A:T.200, A:T.200, A:S.201, A:V.240, A:A.242, A:T.247, A:G.248 pi-Stacking: A:F.244 ANP.44: 22 residues within 4Å: Chain B: D.127, V.129, G.131, D.132, N.164, E.167, T.200, S.201, L.213, V.215, I.237, K.239, V.240, A.242, F.244, T.247, G.248, F.251, L.281 Ligands: MG.23, UNX.28, UNX.43 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.164, B:T.200, B:T.200, B:S.201, B:V.240, B:V.240, B:T.247 pi-Stacking: B:F.244

Links

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Citation

Ismail, S. et al., Crystal structure of a human pyridoxal kinase. To be Published

Release Date

2005-08-09

Peptides

Pyridoxal kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxal kinase

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