SMTL ID : 6bwq.1

LarC2, the C-terminal domain of a cyclometallase involved in the synthesis of the NPN cofactor of lactate racemase, in complex with MnCTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

18 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 2 residues within 4Å: Chain A: E.116 Ligands: CTP.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.116, H2O.1, H2O.2 MN.2: 1 residues within 4Å: Chain A: D.99 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.99, H2O.1 MN.3: 2 residues within 4Å: Chain F: R.46 Ligands: CTP.9 No protein-ligand interaction detected (PLIP) MN.6: 3 residues within 4Å: Chain C: D.13, R.46 Ligands: CTP.4 No protein-ligand interaction detected (PLIP) MN.7: 3 residues within 4Å: Chain B: K.103, E.116 Ligands: CTP.9 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.116, H2O.5 MN.8: 1 residues within 4Å: Chain B: H.128 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.128, H2O.6 MN.12: 2 residues within 4Å: Chain C: E.116 Ligands: CTP.15 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.116, H2O.7, H2O.8 MN.13: 1 residues within 4Å: Chain C: D.99 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.99, H2O.7 MN.14: 2 residues within 4Å: Chain B: R.46 Ligands: CTP.20 No protein-ligand interaction detected (PLIP) MN.17: 3 residues within 4Å: Chain E: D.13, R.46 Ligands: CTP.15 No protein-ligand interaction detected (PLIP) MN.18: 3 residues within 4Å: Chain D: K.103, E.116 Ligands: CTP.20 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.116, H2O.11 MN.19: 1 residues within 4Å: Chain D: H.128 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.128, H2O.11 MN.23: 2 residues within 4Å: Chain E: E.116 Ligands: CTP.26 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.116, H2O.12, H2O.13 MN.24: 1 residues within 4Å: Chain E: D.99 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.99, H2O.12 MN.25: 2 residues within 4Å: Chain D: R.46 Ligands: CTP.31 No protein-ligand interaction detected (PLIP) MN.28: 3 residues within 4Å: Chain A: D.13, R.46 Ligands: CTP.26 No protein-ligand interaction detected (PLIP) MN.29: 3 residues within 4Å: Chain F: K.103, E.116 Ligands: CTP.31 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.116, H2O.16 MN.30: 1 residues within 4Å: Chain F: H.128 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.128, H2O.16

6 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.4: 13 residues within 4Å: Chain A: Y.33, D.34, R.83, R.88, K.103, E.116, Y.117 Chain C: K.43, K.44, R.46 Ligands: MN.1, CL.5, MN.6 22 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A, 9 interactions with chain C Hydrogen bonds: B:E.18, A:D.34, A:R.83, A:R.83, A:K.103, A:K.103 Water bridges: A:R.88, A:R.88, A:Y.117, A:Y.117, A:Y.117, A:Y.117, C:K.43, C:R.46, C:R.46 Salt bridges: A:K.103, C:K.43, C:K.43, C:K.43, C:K.44, C:K.44, C:R.46 CTP.9: 14 residues within 4Å: Chain A: E.18 Chain B: Y.33, L.54, R.83, R.88, K.103, E.116, Y.117 Chain F: K.43, K.44, R.46 Ligands: MN.3, MN.7, CL.10 23 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A, 9 interactions with chain F Hydrogen bonds: B:R.83, B:R.83, B:R.88 Water bridges: B:R.88, B:K.103, B:K.103, B:K.103, B:K.103, B:Y.117, B:Y.117, B:A.118, B:A.118, A:E.18, F:R.46, F:R.46, F:R.77 Salt bridges: B:K.103, F:K.43, F:K.43, F:K.43, F:K.44, F:K.44, F:R.46 CTP.15: 13 residues within 4Å: Chain C: Y.33, D.34, R.83, R.88, K.103, E.116, Y.117 Chain E: K.43, K.44, R.46 Ligands: MN.12, CL.16, MN.17 22 PLIP interactions: 9 interactions with chain E, 12 interactions with chain C, 1 interactions with chain D Water bridges: E:K.43, E:R.46, E:R.46, C:R.88, C:R.88, C:Y.117, C:Y.117, C:Y.117, C:Y.117 Salt bridges: E:K.43, E:K.43, E:K.43, E:K.44, E:K.44, E:R.46, C:K.103 Hydrogen bonds: C:D.34, C:R.83, C:R.83, C:K.103, C:K.103, D:E.18 CTP.20: 14 residues within 4Å: Chain B: K.43, K.44, R.46 Chain C: E.18 Chain D: Y.33, L.54, R.83, R.88, K.103, E.116, Y.117 Ligands: MN.14, MN.18, CL.21 23 PLIP interactions: 13 interactions with chain D, 1 interactions with chain C, 9 interactions with chain B Hydrogen bonds: D:R.83, D:R.83, D:R.88 Water bridges: D:R.88, D:K.103, D:K.103, D:K.103, D:K.103, D:Y.117, D:Y.117, D:A.118, D:A.118, C:E.18, B:R.46, B:R.46, B:R.77 Salt bridges: D:K.103, B:K.43, B:K.43, B:K.43, B:K.44, B:K.44, B:R.46 CTP.26: 13 residues within 4Å: Chain A: K.43, K.44, R.46 Chain E: Y.33, D.34, R.83, R.88, K.103, E.116, Y.117 Ligands: MN.23, CL.27, MN.28 23 PLIP interactions: 13 interactions with chain E, 9 interactions with chain A, 1 interactions with chain F Hydrogen bonds: E:D.34, E:D.34, E:R.83, E:R.83, E:K.103, E:K.103, F:E.18 Water bridges: E:R.88, E:R.88, E:Y.117, E:Y.117, E:Y.117, E:Y.117, A:K.43, A:R.46, A:R.46 Salt bridges: E:K.103, A:K.43, A:K.43, A:K.43, A:K.44, A:K.44, A:R.46 CTP.31: 14 residues within 4Å: Chain D: K.43, K.44, R.46 Chain E: E.18 Chain F: Y.33, L.54, R.83, R.88, K.103, E.116, Y.117 Ligands: MN.25, MN.29, CL.32 24 PLIP interactions: 14 interactions with chain F, 9 interactions with chain D, 1 interactions with chain E Hydrogen bonds: F:R.83, F:R.83, F:R.88, F:E.116 Water bridges: F:R.88, F:K.103, F:K.103, F:K.103, F:K.103, F:Y.117, F:Y.117, F:A.118, F:A.118, D:R.46, D:R.46, D:R.77, E:E.18 Salt bridges: F:K.103, D:K.43, D:K.43, D:K.43, D:K.44, D:K.44, D:R.46

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

CL.5: 3 residues within 4Å: Chain A: R.83 Chain C: R.77 Ligands: CTP.4 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: R.83 Chain F: R.77 Ligands: CTP.9 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: K.50 Chain D: K.50 Chain F: K.50 Ligands: CL.22, CL.33 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: R.83 Chain E: R.77 Ligands: CTP.15 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: R.77 Chain D: R.83 Ligands: CTP.20 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain B: K.50 Chain D: K.50 Chain F: K.50 Ligands: CL.11, CL.33 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain A: R.77 Chain E: R.83 Ligands: CTP.26 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain D: R.77 Chain F: R.83 Ligands: CTP.31 Ligand excluded by PLIP CL.33: 5 residues within 4Å: Chain B: K.50 Chain D: K.50 Chain F: K.50 Ligands: CL.11, CL.22 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Desguin, B. et al., Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase. J. Biol. Chem. (2018)

Release Date

2018-06-20

Peptides

Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

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