SMTL ID : 6p35.1 (1 other biounit)

2.5 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with 2-keto arginine and NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

4 x NWG: 5-[(diaminomethylidene)amino]-2-oxopentanoic acid(Non-covalent)

NWG.1: 8 residues within 4Å: Chain A: W.45, H.46, G.64, A.65, G.66, R.227, H.275 Ligands: NAP.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.45, A:H.46, A:A.65, A:G.66, A:R.227, A:R.227, A:H.275 Salt bridges: A:R.227 NWG.4: 9 residues within 4Å: Chain A: F.10, D.11, W.15, I.279, T.280, R.281, P.282 Chain B: E.131 Ligands: GOL.3 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.10 Hydrogen bonds: A:D.11, A:W.15, A:T.280 Water bridges: A:R.281, B:E.131 Salt bridges: B:E.131 NWG.9: 8 residues within 4Å: Chain B: W.45, H.46, G.64, A.65, G.66, R.227, H.275 Ligands: NAP.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:W.45, B:H.46, B:A.65, B:G.66, B:R.227, B:R.227, B:H.275 Salt bridges: B:R.227 NWG.12: 9 residues within 4Å: Chain A: E.131 Chain B: F.10, D.11, W.15, I.279, T.280, R.281, P.282 Ligands: GOL.11 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.10 Hydrogen bonds: B:D.11, B:W.15, B:T.280 Water bridges: B:R.281, A:E.131 Salt bridges: A:E.131

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.169, Q.176, S.177, F.178, E.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.169, A:Q.176, A:S.177 GOL.3: 5 residues within 4Å: Chain A: D.11, W.14, W.15, P.282 Ligands: NWG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.11, A:D.11 GOL.10: 5 residues within 4Å: Chain B: R.169, Q.176, S.177, F.178, E.183 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.169, B:Q.176, B:S.177 GOL.11: 5 residues within 4Å: Chain B: D.11, W.14, W.15, P.282 Ligands: NWG.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.11

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

NAP.5: 36 residues within 4Å: Chain A: A.65, G.66, V.67, D.68, R.89, M.95, M.99, G.143, A.144, G.145, V.146, L.147, G.148, W.165, S.166, R.167, T.168, K.170, G.180, L.197, L.198, P.199, N.200, E.203, T.204, L.225, A.226, R.227, D.251, V.252, H.275, A.277, A.278, R.310, Y.312 Ligands: NWG.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:A.65, A:L.147, A:A.278 Hydrogen bonds: A:A.144, A:A.144, A:V.146, A:L.147, A:G.148, A:R.167, A:T.168, A:T.168, A:D.251, A:H.275, A:A.277, A:A.278, A:Y.312 Water bridges: A:A.65, A:D.68, A:R.89, A:G.145, A:N.200, A:E.203 Salt bridges: A:R.89, A:R.89, A:K.170 NAP.13: 36 residues within 4Å: Chain B: A.65, G.66, V.67, D.68, R.89, M.95, M.99, G.143, A.144, G.145, V.146, L.147, G.148, W.165, S.166, R.167, T.168, K.170, G.180, L.197, L.198, P.199, N.200, E.203, T.204, L.225, A.226, R.227, D.251, V.252, H.275, A.277, A.278, R.310, Y.312 Ligands: NWG.9 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:A.65, B:L.147, B:A.278 Hydrogen bonds: B:A.144, B:A.144, B:V.146, B:L.147, B:G.148, B:R.167, B:T.168, B:T.168, B:D.251, B:D.251, B:H.275, B:A.277, B:A.278, B:Y.312 Water bridges: B:A.65, B:D.68, B:R.89, B:G.145, B:N.200, B:E.203, B:E.203 Salt bridges: B:R.89, B:R.89, B:K.170

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

SO4.6: 5 residues within 4Å: Chain A: F.111, H.133, R.134, R.159 Chain B: R.281 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.134 Water bridges: A:E.135, A:R.159 Salt bridges: A:H.133, A:R.134, A:R.159, B:R.281 SO4.7: 5 residues within 4Å: Chain A: P.47, P.48, V.49, E.50, K.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.47, A:V.49 Salt bridges: A:K.73 SO4.8: 4 residues within 4Å: Chain A: R.113, L.129, P.130, Y.132 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.113, A:Y.132 Salt bridges: A:R.113 SO4.14: 5 residues within 4Å: Chain A: R.281 Chain B: F.111, H.133, R.134, R.159 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Salt bridges: A:R.281, B:H.133, B:R.134, B:R.159 Hydrogen bonds: B:R.134 Water bridges: B:E.135, B:R.159 SO4.15: 5 residues within 4Å: Chain B: P.47, P.48, V.49, E.50, K.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.47, B:V.49 Salt bridges: B:K.73 SO4.16: 4 residues within 4Å: Chain B: R.113, L.129, P.130, Y.132 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.113, B:Y.132 Salt bridges: B:R.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vuksanovic, N., 2.1 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with glyoxylate and NADP. To Be Published

Release Date

2020-05-27

Peptides

Glyoxylate/hydroxypyruvate reductase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glyoxylate/hydroxypyruvate reductase A

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