SMTL ID : 5ayv.1

Crystal structure of archaeal ketopantoate reductase complexed with coenzyme A and 2-oxopantoate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 22 residues within 4Å: Chain A: L.6, G.7, G.9, S.10, I.11, I.29, G.30, R.31, A.72, V.73, K.74, S.77, A.81, I.98, Q.99, N.100, T.120, N.122, G.123, A.124, E.262 Ligands: ACT.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.11, A:I.11, A:T.120 Hydrogen bonds: A:S.10, A:I.11, A:V.73, A:S.77, A:N.100, A:N.100, A:A.124, A:A.124, A:E.262 Water bridges: A:A.8, A:G.9, A:S.10, A:S.10, A:S.10, A:G.12, A:K.74, A:S.77, A:A.81 Salt bridges: A:R.31, A:K.74, A:K.74

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: W.288, K.292, R.296 Chain B: H.206 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.288, A:K.292 Water bridges: A:R.296 Salt bridges: A:K.292, A:R.296, B:H.206 ACT.3: 4 residues within 4Å: Chain A: L.126, E.128, W.129, R.259 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.126, A:W.129 Hydrogen bonds: A:R.259 Water bridges: A:R.259 ACT.4: 2 residues within 4Å: Chain A: R.31 Ligands: NAP.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.259 ACT.5: 3 residues within 4Å: Chain A: E.272, Y.273, S.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.272 Salt bridges: A:K.269 ACT.10: 5 residues within 4Å: Chain A: H.206 Chain B: W.288, V.289, K.292, R.296 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.289, B:K.292, A:H.206 Salt bridges: B:R.296, A:H.206

1 x COA: COENZYME A(Non-covalent)

COA.6: 19 residues within 4Å: Chain B: L.6, G.7, A.8, G.9, S.10, I.29, G.30, R.31, I.59, Y.60, V.73, K.74, T.80, A.81, C.84, L.126, W.129, R.257, R.259 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:L.6, B:V.73, B:T.80 Hydrogen bonds: B:A.8, B:S.10, B:R.31, B:R.31, B:I.59, B:R.257 Water bridges: B:G.7, B:G.9, B:S.10, B:S.10, B:S.10, B:I.11, B:R.31, B:K.74, B:L.126, B:R.257, B:R.259, B:R.259 Salt bridges: B:R.31, B:K.74, B:R.257, B:R.259, B:R.259 pi-Cation interactions: B:R.31

1 x KPL: KETOPANTOATE(Non-covalent)

KPL.7: 13 residues within 4Å: Chain B: N.100, T.121, N.122, G.123, K.180, N.184, I.187, N.188, N.198, T.240, N.247, N.249, S.250 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.187, B:T.240 Hydrogen bonds: B:N.100, B:K.180, B:N.184, B:N.188, B:N.198, B:N.247, B:S.250 Water bridges: B:S.250, B:S.250

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 6 residues within 4Å: Chain B: A.135, G.136, K.137, E.242, R.243, T.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.137, B:R.243, B:R.245 MPD.9: 5 residues within 4Å: Chain B: G.47, A.48, W.134, A.135, E.246 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aikawa, Y. et al., Crystal structure of archaeal ketopantoate reductase complexed with coenzyme a and 2-oxopantoate provides structural insights into feedback regulation. Proteins (2016)

Release Date

2016-01-27

Peptides

2-dehydropantoate 2-reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-dehydropantoate 2-reductase