SMTL ID : 5kvs.1

Substrate Analog and NADP+ bound structure of Irp3, a Thiazolinyl Imine Reductase from Yersinia enterocolitica

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 26 residues within 4Å: Chain A: V.33, G.34, A.35, K.36, F.37, G.38, L.58, A.59, Q.60, G.61, S.62, R.64, S.65, V.93, V.94, R.95, A.99, A.102, L.106, E.120, H.121, P.122, Q.182, L.183, D.239 Ligands: 6XR.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:F.37 Hydrogen bonds: A:A.35, A:K.36, A:F.37, A:Q.60, A:G.61, A:S.62, A:S.62, A:R.64, A:S.65, A:R.95, A:H.121, A:Q.182 Water bridges: A:K.36, A:G.38, A:Q.60, A:R.95, A:R.95, A:R.95, A:S.96, A:S.96 Salt bridges: A:R.64, A:R.95 NAP.5: 28 residues within 4Å: Chain B: V.33, G.34, A.35, K.36, F.37, G.38, L.58, A.59, Q.60, G.61, S.62, R.64, S.65, V.93, V.94, R.95, S.96, A.99, A.102, L.106, E.120, H.121, P.122, F.147, Y.148, L.183, D.239 Ligands: 6XR.6 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:A.35, B:K.36, B:F.37, B:Q.60, B:G.61, B:S.62, B:S.62, B:R.64, B:R.95, B:E.120, B:H.121, B:Y.148, B:Y.148 Water bridges: B:Q.60, B:R.95, B:R.95, B:E.120, B:H.121, B:D.239, B:D.239, B:D.239 Salt bridges: B:R.64, B:R.95 pi-Stacking: B:F.37

2 x 6XR: (4~{R})-2-[2-(2-hydroxyphenyl)-1,3-thiazol-4-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid(Non-covalent)

6XR.2: 15 residues within 4Å: Chain A: K.36, F.37, E.39, M.40, Y.148, Q.182, L.183, D.239, M.240, M.245 Chain B: L.272, V.274, H.277, L.284 Ligands: NAP.1 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:K.36, B:V.274, B:H.277, B:L.284, B:L.284 Hydrogen bonds: A:Y.148, A:Y.148 6XR.6: 15 residues within 4Å: Chain A: L.272, V.274, H.277, L.284 Chain B: K.36, F.37, E.39, M.40, Y.148, Q.182, L.183, D.239, M.240, M.245 Ligands: NAP.5 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.274, A:L.284, A:L.284, A:L.284, B:K.36 Hydrogen bonds: B:Y.148 Water bridges: B:D.239

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 9 residues within 4Å: Chain A: S.270, S.271, L.272, F.273, L.291, R.292, D.293 Chain B: W.306, H.370 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.273, A:L.291, A:D.293, A:D.293 Water bridges: A:R.292 EDO.7: 9 residues within 4Å: Chain A: W.306, H.370 Chain B: S.270, S.271, L.272, F.273, L.291, R.292, D.293 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.273, B:F.273, B:L.291, B:L.291, B:D.293 Water bridges: B:R.292

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 7 residues within 4Å: Chain A: Q.230, Y.232, H.241, S.242, L.243, L.365 Chain B: P.253 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.232, A:H.241 Water bridges: A:H.241, A:S.242 FMT.8: 7 residues within 4Å: Chain A: P.253 Chain B: Q.230, Y.232, H.241, S.242, L.243, L.365 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.232, B:Y.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meneely, K.M. et al., Holo Structure and Steady State Kinetics of the Thiazolinyl Imine Reductases for Siderophore Biosynthesis. Biochemistry (2016)

Release Date

2016-09-21

Peptides

Irp3 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Irp3 protein

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