SMTL ID : 4m1q.1

Crystal structure of L-lactate dehydrogenase from Bacillus selenitireducens MLS10, NYSGRC Target 029814.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: R.177, H.192, Y.194 Chain B: N.190, H.192, G.213, S.214 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Y.194, B:N.190, B:N.190 Water bridges: A:R.177, A:R.177, B:R.189, B:R.189 Salt bridges: A:R.177, A:H.192, B:H.192 PO4.5: 7 residues within 4Å: Chain A: N.190, H.192, G.213, S.214 Chain B: R.177, H.192, Y.194 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:N.190, A:N.190, A:G.213 Salt bridges: A:H.192, B:R.177, B:H.192 Water bridges: B:R.177, B:R.177, B:H.192, B:H.192, B:Y.194 PO4.9: 7 residues within 4Å: Chain C: R.177, H.192, Y.194 Chain D: N.190, H.192, G.213, S.214 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Y.194, C:Y.194, D:N.190, D:N.190 Water bridges: C:R.177, C:R.177, D:R.189, D:R.189 Salt bridges: C:R.177, C:H.192, D:H.192 PO4.13: 7 residues within 4Å: Chain C: N.190, H.192, G.213, S.214 Chain D: R.177, H.192, Y.194 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:N.190, C:N.190, C:G.213, D:Y.194 Salt bridges: C:H.192, D:R.177, D:H.192 Water bridges: D:R.177, D:R.177, D:H.192, D:Y.194

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

MPD.2: 7 residues within 4Å: Chain A: M.70, N.73, H.74 Chain D: F.178, L.179, N.239, A.243 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Water bridges: A:N.73 Hydrophobic interactions: D:F.178 Hydrogen bonds: D:N.239, D:N.239 MPD.3: 3 residues within 4Å: Chain A: D.234, F.237, V.238 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.237 MPD.4: 2 residues within 4Å: Chain A: G.103, I.122 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.122 Hydrogen bonds: A:G.103 Water bridges: A:G.103, A:G.103, A:A.105 MPD.6: 6 residues within 4Å: Chain B: M.70, N.73, H.74 Chain C: R.175, F.178, A.243 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:R.175, C:F.178, C:A.243 Hydrogen bonds: B:H.74 Water bridges: B:N.73 MPD.7: 5 residues within 4Å: Chain B: A.120, N.121, K.124, F.156, I.335 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.120, B:K.124, B:K.124, B:F.156 Water bridges: B:G.125 MPD.8: 3 residues within 4Å: Chain B: W.207, N.230, D.234 2 PLIP interactions: 2 interactions with chain B Water bridges: B:W.207, B:D.234 MPD.10: 7 residues within 4Å: Chain B: F.178, L.179, N.239, A.243 Chain C: M.70, N.73, H.74 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.178 Hydrogen bonds: B:N.239, B:N.239 Water bridges: C:N.73 MPD.11: 3 residues within 4Å: Chain C: D.234, F.237, V.238 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.237 MPD.12: 2 residues within 4Å: Chain C: G.103, I.122 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.122 Hydrogen bonds: C:G.103 Water bridges: C:G.103, C:G.103, C:A.105 MPD.14: 6 residues within 4Å: Chain A: R.175, F.178, A.243 Chain D: M.70, N.73, H.74 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:H.74 Water bridges: D:N.73 Hydrophobic interactions: A:R.175, A:F.178, A:A.243 MPD.15: 5 residues within 4Å: Chain D: A.120, N.121, K.124, F.156, I.335 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.120, D:K.124, D:K.124, D:F.156 Water bridges: D:G.125 MPD.16: 3 residues within 4Å: Chain D: W.207, N.230, D.234 2 PLIP interactions: 2 interactions with chain D Water bridges: D:W.207, D:D.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malashkevich, V.N. et al., Crystal structure of L-lactate dehydrogenase from Bacillus selenitireducens MLS10, NYSGRC Target 029814. To be Published

Release Date

2013-08-21

Peptides

L-lactate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-lactate dehydrogenase