SMTL ID : 6abi.1

The apo-structure of D-lactate dehydrogenase from Fusobacterium nucleatum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: V.58, R.59 Chain D: L.56, K.57, V.58 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: P.232, L.233, R.260 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: V.335, T.336, N.339 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: H.128, K.179 Chain B: Y.168 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: Y.168 Chain B: H.128, K.179 Ligands: GOL.14 Ligand excluded by PLIP SO4.7: 8 residues within 4Å: Chain B: C.102, A.103, R.121, P.123, A.124, R.260, H.321 Ligands: GOL.13 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: P.232, L.233, R.260 Ligands: GOL.15 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain B: T.336, N.339 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain B: L.56, K.57, V.58 Chain C: V.58, R.59 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: P.232, L.233, R.260 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: V.335, T.336, N.339 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain C: H.128, K.179 Chain D: Y.168 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: Y.168 Chain D: H.128, K.179 Ligands: GOL.30 Ligand excluded by PLIP SO4.23: 8 residues within 4Å: Chain D: C.102, A.103, R.121, P.123, A.124, R.260, H.321 Ligands: GOL.29 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain D: P.232, L.233, R.260 Ligands: GOL.31 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain D: T.336, N.339 Ligand excluded by PLIP

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: V.141, N.142, K.144, M.163, G.164, G.252, I.254, G.279 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain A: D.166 Chain B: S.126, P.127, H.128, A.129, E.328, A.329, A.332 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain B: G.178, D.199, L.200, F.201, P.232 Ligands: GOL.15 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain B: V.141, N.142, K.144, G.164, G.252, I.254, G.279 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain B: Y.125, I.130, I.180, T.258, G.259, R.260, H.321 Ligands: SO4.7 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain B: Y.125, P.127, K.179 Ligands: SO4.6 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain B: P.232 Ligands: SO4.8, GOL.11 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain B: V.122, P.123, A.124, Y.125, A.332, I.333, T.336 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain C: V.141, N.142, K.144, M.163, G.164, G.252, I.254, G.279 Ligand excluded by PLIP GOL.26: 8 residues within 4Å: Chain C: D.166 Chain D: S.126, P.127, H.128, A.129, E.328, A.329, A.332 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain D: G.178, D.199, L.200, F.201, P.232 Ligands: GOL.31 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain D: V.141, N.142, K.144, G.164, G.252, I.254, G.279 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain D: Y.125, I.130, I.180, T.258, G.259, R.260, H.321 Ligands: SO4.23 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain D: Y.125, P.127, K.179 Ligands: SO4.22 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain D: P.232 Ligands: SO4.24, GOL.27 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain D: V.122, P.123, A.124, Y.125, A.332, I.333, T.336 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furukawa, N. et al., Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria. Biochemistry (2018)

Release Date

2018-09-19

Peptides

D-lactate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

D-lactate dehydrogenase

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