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

Structure of human Phosphogluconate Dehydrogenase in complex with NADPH at 2.53A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 25 residues within 4Å: Chain A: G.473, H.475, S.500, S.501, Y.503 Chain B: G.32, L.33, A.34, V.35, M.36, N.55, R.56, T.57, K.60, L.96, V.97, K.98, A.99, A.102, F.106, G.124, N.125, V.150, G.153 Ligands: CL.8 33 PLIP interactions: 26 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:L.33, B:A.34, B:M.36, B:N.55, B:N.55, B:R.56, B:T.57, B:T.57, B:V.97, B:K.98, B:A.99, B:N.125, B:N.125, A:G.473, A:S.500, A:S.501, A:Y.503 Water bridges: B:G.37, B:R.56, B:R.56, B:R.56, B:K.60, B:D.105, B:N.125, B:K.283, B:K.283, A:S.501, A:Y.503, A:Y.503 Salt bridges: B:R.56, B:K.60 pi-Cation interactions: B:R.56, B:R.56 NAP.7: 25 residues within 4Å: Chain A: G.32, L.33, A.34, V.35, M.36, N.55, R.56, T.57, K.60, L.96, V.97, K.98, A.99, A.102, F.106, G.124, N.125, V.150, G.153 Chain B: G.473, H.475, S.500, S.501, Y.503 Ligands: CL.2 29 PLIP interactions: 24 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:L.33, A:M.36, A:N.55, A:N.55, A:T.57, A:T.57, A:V.97, A:K.98, A:A.99, A:N.125, B:G.473, B:S.500, B:S.501, B:Y.503, B:Y.503 Water bridges: A:A.34, A:G.37, A:R.56, A:R.56, A:R.56, A:N.125, A:N.125, A:K.283, A:K.283 Salt bridges: A:R.56, A:K.60, A:K.283 pi-Cation interactions: A:R.56, A:R.56

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: N.125, K.206, N.210 Ligands: NAP.7 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: W.172, K.176, D.194 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: K.325 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: N.125, K.206, N.210 Ligands: NAP.1 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: W.172, K.176 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: K.325 Ligand excluded by PLIP

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

SO4.3: 6 residues within 4Å: Chain A: Y.214, Q.282, K.283, R.310 Chain B: R.469, H.475 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.210, A:Y.214, A:Y.214, A:K.283 Water bridges: A:N.125, A:E.213, A:R.310 Salt bridges: A:R.310, B:R.469, B:H.475 SO4.4: 2 residues within 4Å: Chain A: K.270, H.271 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.271 Water bridges: A:G.269, A:H.271 Salt bridges: A:H.271 SO4.10: 6 residues within 4Å: Chain A: R.469, H.475 Chain B: Y.214, Q.282, K.283, R.310 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Salt bridges: A:R.469, A:H.475, B:R.310 Hydrogen bonds: B:Y.214, B:K.283 Water bridges: B:N.125, B:R.310, B:R.310 SO4.11: 2 residues within 4Å: Chain B: K.270, H.271 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.271 Water bridges: B:Q.235, B:G.269, B:H.271 Salt bridges: B:H.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ng, S.S. et al., Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A. To be Published

Release Date

2009-09-01

Peptides

6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING

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