SMTL ID : 2ldb.1

STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: L.151, R.155, H.179, A.223, T.233 Ligands: NAD.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.233 Salt bridges: A:R.155, A:H.179 SO4.2: 7 residues within 4Å: Chain A: G.29, I.30, A.31, D.32, P.59, K.60 Chain B: H.250 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.250 Hydrogen bonds: A:G.29 SO4.4: 6 residues within 4Å: Chain B: L.151, R.155, H.179, A.223, T.233 Ligands: NAD.6 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.155, B:H.179 SO4.5: 7 residues within 4Å: Chain A: H.250 Chain B: G.29, I.30, A.31, D.32, P.59, K.60 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.29 Water bridges: B:K.60 Salt bridges: A:H.250 SO4.8: 6 residues within 4Å: Chain C: L.151, R.155, H.179, A.223, T.233 Ligands: NAD.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.233 Salt bridges: C:R.155, C:H.179 SO4.9: 7 residues within 4Å: Chain C: G.29, I.30, A.31, D.32, P.59, K.60 Chain D: H.250 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.29 Salt bridges: D:H.250 SO4.12: 6 residues within 4Å: Chain D: L.151, R.155, H.179, A.223, T.233 Ligands: NAD.14 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.155, D:H.179 SO4.13: 7 residues within 4Å: Chain C: H.250 Chain D: G.29, I.30, A.31, D.32, P.59, K.60 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:H.250 Hydrogen bonds: D:G.29

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

NAD.3: 22 residues within 4Å: Chain A: I.12, G.13, A.14, G.15, F.16, V.17, D.38, A.39, N.40, C.81, A.82, G.83, I.102, A.122, T.123, N.124, S.147, L.151, H.179, T.233, I.237 Ligands: SO4.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.17, A:I.237, A:I.237 Hydrogen bonds: A:A.14, A:F.16, A:V.17, A:A.39, A:N.40, A:A.122, A:N.124, A:N.124, A:S.147 Water bridges: A:N.40 NAD.6: 22 residues within 4Å: Chain B: I.12, G.13, A.14, G.15, F.16, V.17, D.38, A.39, N.40, C.81, A.82, G.83, I.102, A.122, T.123, N.124, S.147, L.151, H.179, T.233, I.237 Ligands: SO4.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.17, B:I.237, B:I.237 Hydrogen bonds: B:A.14, B:F.16, B:V.17, B:A.39, B:N.40, B:A.122, B:N.124, B:N.124, B:S.147 NAD.10: 22 residues within 4Å: Chain C: I.12, G.13, A.14, G.15, F.16, V.17, D.38, A.39, N.40, C.81, A.82, G.83, I.102, A.122, T.123, N.124, S.147, L.151, H.179, T.233, I.237 Ligands: SO4.8 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.17, C:I.237, C:I.237 Hydrogen bonds: C:A.14, C:F.16, C:V.17, C:A.39, C:N.40, C:A.122, C:N.124, C:N.124, C:S.147 NAD.14: 22 residues within 4Å: Chain D: I.12, G.13, A.14, G.15, F.16, V.17, D.38, A.39, N.40, C.81, A.82, G.83, I.102, A.122, T.123, N.124, S.147, L.151, H.179, T.233, I.237 Ligands: SO4.12 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:V.17, D:I.237, D:I.237 Hydrogen bonds: D:A.14, D:F.16, D:V.17, D:A.39, D:N.40, D:A.122, D:N.124, D:N.124, D:S.147

2 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.7: 11 residues within 4Å: Chain B: R.157, Q.169, N.170, H.172, G.193, I.255 Chain C: R.157, Q.169, N.170, H.172, I.255 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:Q.169, B:V.171, C:R.157, C:Q.169, C:N.170, C:H.172, C:I.255 Salt bridges: B:R.157, B:H.172, B:H.172, C:R.157, C:H.172, C:H.172 FBP.11: 11 residues within 4Å: Chain A: R.157, Q.169, N.170, H.172, G.193, I.255 Chain D: R.157, Q.169, N.170, H.172, I.255 13 PLIP interactions: 7 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:R.157, D:Q.169, D:N.170, D:I.255, A:Q.169, A:V.171 Salt bridges: D:R.157, D:H.172, D:H.172, A:R.157, A:H.172, A:H.172 Water bridges: A:Q.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piontek, K. et al., Structure determination and refinement of Bacillus stearothermophilus lactate dehydrogenase. Proteins (1990)

Release Date

1989-07-12

Peptides

L-LACTATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-LACTATE DEHYDROGENASE

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