SMTL ID : 4q3n.1

Crystal structure of MGS-M5, a lactate dehydrogenase enzyme from a Medee basin deep-sea metagenome library

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: I.198, M.201, I.204, S.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.198 Water bridges: A:D.202 NA.18: 4 residues within 4Å: Chain B: I.198, M.201, I.204, S.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.201 NA.35: 4 residues within 4Å: Chain C: I.198, M.201, I.204, S.205 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.204 Water bridges: C:D.202 NA.52: 4 residues within 4Å: Chain D: I.198, M.201, I.204, S.205 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.204

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 1 residues within 4Å: Chain A: G.12 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: N.3, S.4, K.5, E.30 Chain B: R.2 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain B: G.12 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: R.2 Chain B: N.3, S.4, K.5, E.30 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain C: G.12 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain C: N.3, S.4, K.5, E.30 Chain D: R.2 Ligand excluded by PLIP CL.53: 1 residues within 4Å: Chain D: G.12 Ligand excluded by PLIP CL.54: 5 residues within 4Å: Chain C: R.2 Chain D: N.3, S.4, K.5, E.30 Ligand excluded by PLIP

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

ACT.4: 5 residues within 4Å: Chain A: K.192, V.197, M.201 Chain D: H.284, V.286 Ligand excluded by PLIP ACT.5: 8 residues within 4Å: Chain A: S.158, Q.159, H.162, I.163, D.164 Chain C: K.58 Chain D: E.249, N.250 Ligand excluded by PLIP ACT.6: 7 residues within 4Å: Chain A: S.4, T.27, R.57, F.246, N.247 Chain B: R.57 Ligands: ACT.23 Ligand excluded by PLIP ACT.7: 2 residues within 4Å: Chain A: Q.159, Y.160 Ligand excluded by PLIP ACT.8: 3 residues within 4Å: Chain A: L.214, K.215, D.218 Ligand excluded by PLIP ACT.9: 6 residues within 4Å: Chain A: V.14, N.121, L.148, H.176, T.230, I.234 Ligand excluded by PLIP ACT.21: 5 residues within 4Å: Chain B: K.192, V.197, M.201 Chain C: H.284, V.286 Ligand excluded by PLIP ACT.22: 8 residues within 4Å: Chain B: S.158, Q.159, H.162, I.163, D.164 Chain C: E.249, N.250 Chain D: K.58 Ligand excluded by PLIP ACT.23: 7 residues within 4Å: Chain A: R.57 Chain B: S.4, T.27, R.57, F.246, N.247 Ligands: ACT.6 Ligand excluded by PLIP ACT.24: 2 residues within 4Å: Chain B: Q.159, Y.160 Ligand excluded by PLIP ACT.25: 3 residues within 4Å: Chain B: L.214, K.215, D.218 Ligand excluded by PLIP ACT.26: 6 residues within 4Å: Chain B: V.14, N.121, L.148, H.176, T.230, I.234 Ligand excluded by PLIP ACT.38: 5 residues within 4Å: Chain B: H.284, V.286 Chain C: K.192, V.197, M.201 Ligand excluded by PLIP ACT.39: 8 residues within 4Å: Chain A: K.58 Chain B: E.249, N.250 Chain C: S.158, Q.159, H.162, I.163, D.164 Ligand excluded by PLIP ACT.40: 7 residues within 4Å: Chain C: S.4, T.27, R.57, F.246, N.247 Chain D: R.57 Ligands: ACT.57 Ligand excluded by PLIP ACT.41: 2 residues within 4Å: Chain C: Q.159, Y.160 Ligand excluded by PLIP ACT.42: 3 residues within 4Å: Chain C: L.214, K.215, D.218 Ligand excluded by PLIP ACT.43: 6 residues within 4Å: Chain C: V.14, N.121, L.148, H.176, T.230, I.234 Ligand excluded by PLIP ACT.55: 5 residues within 4Å: Chain A: H.284, V.286 Chain D: K.192, V.197, M.201 Ligand excluded by PLIP ACT.56: 8 residues within 4Å: Chain A: E.249, N.250 Chain B: K.58 Chain D: S.158, Q.159, H.162, I.163, D.164 Ligand excluded by PLIP ACT.57: 7 residues within 4Å: Chain C: R.57 Chain D: S.4, T.27, R.57, F.246, N.247 Ligands: ACT.40 Ligand excluded by PLIP ACT.58: 2 residues within 4Å: Chain D: Q.159, Y.160 Ligand excluded by PLIP ACT.59: 3 residues within 4Å: Chain D: L.214, K.215, D.218 Ligand excluded by PLIP ACT.60: 6 residues within 4Å: Chain D: V.14, N.121, L.148, H.176, T.230, I.234 Ligand excluded by PLIP

8 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 5 residues within 4Å: Chain A: N.113, H.137, S.139, R.140 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.139, A:S.139, A:R.140 PGE.11: 5 residues within 4Å: Chain A: K.105, K.132, E.133, S.134, G.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.105, A:E.133 Water bridges: A:Y.314 PGE.27: 5 residues within 4Å: Chain B: N.113, H.137, S.139, R.140 Ligands: GOL.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.139, B:S.139, B:R.140 PGE.28: 5 residues within 4Å: Chain B: K.105, K.132, E.133, S.134, G.135 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.105, B:E.133 PGE.44: 5 residues within 4Å: Chain C: N.113, H.137, S.139, R.140 Ligands: GOL.47 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.139, C:S.139, C:R.140 PGE.45: 5 residues within 4Å: Chain C: K.105, K.132, E.133, S.134, G.135 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.105, C:E.133 Water bridges: C:Y.314 PGE.61: 5 residues within 4Å: Chain D: N.113, H.137, S.139, R.140 Ligands: GOL.64 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.139, D:S.139, D:R.140 PGE.62: 5 residues within 4Å: Chain D: K.105, K.132, E.133, S.134, G.135 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.105, D:E.133

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 5 residues within 4Å: Chain A: S.185, N.186, K.289 Chain D: P.193, D.196 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain A: N.3, D.71, A.72, N.113, G.114 Chain B: M.1 Ligands: PGE.10 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain A: N.291, E.292 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain A: D.35, K.38, G.64, D.65, Y.66 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain A: M.108, G.111, F.112, N.113 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain B: S.185, N.186, K.289 Chain C: P.193, D.196 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain A: M.1 Chain B: N.3, D.71, A.72, N.113, G.114 Ligands: PGE.27 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain B: N.291, E.292 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain B: D.35, K.38, G.64, D.65, Y.66 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain B: M.108, G.111, F.112, N.113 Ligand excluded by PLIP GOL.46: 5 residues within 4Å: Chain B: P.193, D.196 Chain C: S.185, N.186, K.289 Ligand excluded by PLIP GOL.47: 7 residues within 4Å: Chain C: N.3, D.71, A.72, N.113, G.114 Chain D: M.1 Ligands: PGE.44 Ligand excluded by PLIP GOL.48: 2 residues within 4Å: Chain C: N.291, E.292 Ligand excluded by PLIP GOL.49: 5 residues within 4Å: Chain C: D.35, K.38, G.64, D.65, Y.66 Ligand excluded by PLIP GOL.50: 4 residues within 4Å: Chain C: M.108, G.111, F.112, N.113 Ligand excluded by PLIP GOL.63: 5 residues within 4Å: Chain A: P.193, D.196 Chain D: S.185, N.186, K.289 Ligand excluded by PLIP GOL.64: 7 residues within 4Å: Chain C: M.1 Chain D: N.3, D.71, A.72, N.113, G.114 Ligands: PGE.61 Ligand excluded by PLIP GOL.65: 2 residues within 4Å: Chain D: N.291, E.292 Ligand excluded by PLIP GOL.66: 5 residues within 4Å: Chain D: D.35, K.38, G.64, D.65, Y.66 Ligand excluded by PLIP GOL.67: 4 residues within 4Å: Chain D: M.108, G.111, F.112, N.113 Ligand excluded by PLIP

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.17: 5 residues within 4Å: Chain A: G.261, Y.263, D.264, C.265, D.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.261 Water bridges: A:G.261, A:V.262, A:D.267 TRS.34: 5 residues within 4Å: Chain B: G.261, Y.263, D.264, C.265, D.267 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.261 Water bridges: B:G.261, B:V.262, B:D.267 TRS.51: 5 residues within 4Å: Chain C: G.261, Y.263, D.264, C.265, D.267 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.261 Water bridges: C:G.261, C:V.262, C:D.267 TRS.68: 5 residues within 4Å: Chain D: G.261, Y.263, D.264, C.265, D.267 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.261 Water bridges: D:G.261, D:V.262, D:D.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alcaide, M. et al., Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats. Environ Microbiol (2015)

Release Date

2015-02-25

Peptides

MGS-M5: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

MGS-M5