SMTL ID : 7wvs.1

The structure of FinI complex with SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 17 residues within 4Å: Chain A: G.190, M.203, M.207, G.242, G.243, A.244, D.268, L.269, V.272, I.292, D.293, F.294, H.295, R.309, R.310, I.311, D.314 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.244 Hydrogen bonds: A:G.242, A:A.244, A:L.269, A:D.293, A:F.294 Water bridges: A:T.188, A:G.190, A:G.190, A:G.243, A:T.248, A:T.248, A:R.309, A:R.309, A:R.310 Salt bridges: A:H.216, A:R.309, A:R.310, A:D.314 pi-Stacking: A:F.294 SAM.29: 13 residues within 4Å: Chain B: G.242, G.243, A.244, D.268, L.269, I.292, D.293, F.294, H.295, R.309, R.310, I.311, D.314 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.242, B:D.293, B:F.294 Water bridges: B:T.248, B:R.309 Salt bridges: B:R.309 pi-Stacking: B:F.294

33 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: D.149, E.150, P.153, K.178, E.182, R.199 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: K.44, Q.47, D.48, W.350 Chain B: T.114, R.130 Ligand excluded by PLIP EDO.5: 1 residues within 4Å: Chain A: R.26 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: E.37, G.41, K.44, Q.213, W.350 Ligands: EDO.7, EDO.10 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: E.37, S.212, Q.213, F.351 Chain B: D.55, A.58 Ligands: EDO.6 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: R.373, T.376, A.377, L.381, R.382, I.383 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: G.172, R.173, L.174, E.319 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: G.41, K.44, Q.45, D.48, W.350 Ligands: EDO.6 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: M.60, G.63, F.64 Chain B: M.60, G.63, F.64 Ligands: SO4.27 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain A: Q.277 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: C.253, P.257, I.259, P.260, I.261 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: Q.34, E.37, A.38 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: Y.220, W.224, V.398 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: R.89, E.91 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: V.343, T.344, G.345, Y.388, E.393 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: G.218, F.219, Y.388, S.389, D.390 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: N.138, L.140 Chain B: P.53 Ligands: GOL.21 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: A.68, R.71, Y.148 Chain B: L.155, L.156, P.159 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: H.196, P.197, E.198, R.199 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: G.172, R.173, L.174, E.319 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain B: S.10, L.11 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: L.145, D.149, R.199, N.202 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: D.48, A.49, V.50, Y.51, L.52 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain A: L.156, P.159 Chain B: Y.148, D.149 Ligands: SO4.25 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain B: T.344, T.368, E.369, Y.388 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain B: Y.220, D.221, F.222, S.223, E.255, T.256 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: T.384, G.385, H.387, V.398 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain B: D.84, T.85, R.132 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain B: T.164, Y.165, F.180, P.185 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain B: Q.45, D.48, A.49 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain A: P.153 Chain B: A.157, R.160 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain B: R.173, T.188, V.189, D.314, I.362 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain B: R.173, T.188, G.190 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: K.296, E.297, Q.298, Q.301, H.326, A.329, A.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.298, A:Q.298, A:Q.301 GOL.12: 8 residues within 4Å: Chain A: S.194, R.195, H.196, P.197, T.200, G.271, Q.274, M.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.200, A:T.200 GOL.21: 5 residues within 4Å: Chain A: M.210, A.211, S.212 Chain B: R.54 Ligands: EDO.20 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.210, A:A.211, A:S.212, A:S.212, B:R.54 GOL.22: 4 residues within 4Å: Chain A: D.149, E.150, E.198, R.199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.149, A:E.150 Water bridges: A:N.202, A:N.202 GOL.36: 3 residues within 4Å: Chain B: T.128, A.129, R.132 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.129, B:R.132, B:R.132

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

SO4.24: 3 residues within 4Å: Chain A: R.71, L.74, H.75 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.71, A:H.75, A:K.77 SO4.25: 4 residues within 4Å: Chain A: L.156, R.160 Ligands: SO4.26, EDO.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.156 Salt bridges: A:R.160 SO4.26: 3 residues within 4Å: Chain A: R.160, F.180 Ligands: SO4.25 No protein-ligand interaction detected (PLIP) SO4.27: 7 residues within 4Å: Chain A: D.56, M.60 Chain B: G.63, T.66, A.67, W.144 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.66, B:W.144 Water bridges: B:R.130 SO4.45: 4 residues within 4Å: Chain B: H.196, P.197, E.198, R.199 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.198, B:R.199 Water bridges: B:R.199, B:R.199 Salt bridges: B:H.196 SO4.46: 2 residues within 4Å: Chain B: R.71, H.75 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.71, B:H.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, J. et al., The structure of FinI complex with SAM. To Be Published

Release Date

2023-02-15

Peptides

Methyltransf_2 domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyltransf_2 domain-containing protein

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