SMTL ID : 9ldb.1

DESIGN AND SYNTHESIS OF NEW ENZYMES BASED ON THE LACTATE DEHYDROGENASE FRAMEWORK

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAD.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.100, A:N.138 Salt bridges: A:R.106, A:R.169, A:H.193 SO4.2: 3 residues within 4Å: Chain A: H.186 Chain C: R.171, H.186 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Water bridges: C:H.186, C:W.188, A:H.186 Salt bridges: C:R.171, C:H.186, A:H.186 SO4.4: 4 residues within 4Å: Chain B: S.184, H.186 Chain D: R.171, H.186 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Water bridges: B:H.186, D:R.171, D:W.188 Salt bridges: B:H.186, D:R.171, D:H.186 SO4.7: 9 residues within 4Å: Chain C: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAD.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.100, C:N.138 Salt bridges: C:R.106, C:R.169, C:H.193 SO4.8: 3 residues within 4Å: Chain A: R.171, H.186 Chain C: H.186 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Water bridges: C:H.186, A:H.186, A:W.188 Salt bridges: C:H.186, A:R.171, A:H.186 SO4.10: 4 residues within 4Å: Chain B: R.171, H.186 Chain D: S.184, H.186 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Water bridges: B:R.171, B:W.188, D:H.186 Salt bridges: B:R.171, B:H.186, D:H.186

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 25 residues within 4Å: Chain A: G.27, G.29, A.30, V.31, D.52, V.53, M.54, T.95, A.96, G.97, A.98, R.99, N.113, I.116, F.119, I.120, V.136, S.137, N.138, S.161, L.165, H.193, T.248, I.252 Ligands: SO4.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.31, A:I.252 Hydrogen bonds: A:A.30, A:V.31, A:V.53, A:G.97, A:N.113, A:V.136, A:N.138, A:N.138, A:S.161 Water bridges: A:G.29, A:G.32, A:Y.83, A:R.99, A:Q.100 Salt bridges: A:R.99, A:R.99 NAD.5: 24 residues within 4Å: Chain B: G.29, A.30, V.31, D.52, V.53, M.54, T.95, A.96, G.97, A.98, R.99, N.113, I.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: OXM.6 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:V.31, B:I.252, B:I.252 Hydrogen bonds: B:A.30, B:V.31, B:V.53, B:G.97, B:A.98, B:N.113, B:V.136, B:N.138, B:N.138, B:S.161 Water bridges: B:G.29, B:G.32, B:R.99, B:Q.100 Salt bridges: B:R.99, B:R.99 NAD.9: 25 residues within 4Å: Chain C: G.27, G.29, A.30, V.31, D.52, V.53, M.54, T.95, A.96, G.97, A.98, R.99, N.113, I.116, F.119, I.120, V.136, S.137, N.138, S.161, L.165, H.193, T.248, I.252 Ligands: SO4.7 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:V.31, C:I.252 Hydrogen bonds: C:A.30, C:V.31, C:V.53, C:G.97, C:N.113, C:V.136, C:N.138, C:N.138, C:S.161 Water bridges: C:G.29, C:G.32, C:Y.83, C:R.99, C:Q.100 Salt bridges: C:R.99, C:R.99 NAD.11: 24 residues within 4Å: Chain D: G.29, A.30, V.31, D.52, V.53, M.54, T.95, A.96, G.97, A.98, R.99, N.113, I.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: OXM.12 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:V.31, D:I.252, D:I.252 Hydrogen bonds: D:A.30, D:V.31, D:V.53, D:G.97, D:A.98, D:N.113, D:V.136, D:N.138, D:N.138, D:S.161 Water bridges: D:G.29, D:G.32, D:R.99, D:Q.100 Salt bridges: D:R.99, D:R.99

2 x OXM: OXAMIC ACID(Non-covalent)

OXM.6: 8 residues within 4Å: Chain B: Q.100, R.106, N.138, R.169, H.193, A.238, T.248 Ligands: NAD.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.100, B:R.106, B:N.138, B:T.248, B:T.248, B:T.248 Water bridges: B:T.248 Salt bridges: B:R.106, B:R.169, B:H.193 OXM.12: 8 residues within 4Å: Chain D: Q.100, R.106, N.138, R.169, H.193, A.238, T.248 Ligands: NAD.11 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:Q.100, D:R.106, D:N.138, D:T.248, D:T.248, D:T.248 Water bridges: D:T.248 Salt bridges: D:R.106, D:R.169, D:H.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dunn, C.R. et al., Design and synthesis of new enzymes based on the lactate dehydrogenase framework. Philos.Trans.R.Soc.London,Ser.B (1991)

Release Date

1993-10-31

Peptides

LACTATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

LACTATE DEHYDROGENASE

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