SMTL ID : 7wuy.1

The crystal structure of FinI in complex with SAM and fischerin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: H.196, P.197, E.198, R.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.198, A:R.199 SO4.31: 4 residues within 4Å: Chain B: H.196, P.197, E.198, R.199 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.198, B:R.199 Water bridges: B:R.199 Salt bridges: B:H.196 SO4.32: 6 residues within 4Å: Chain B: R.173, T.188, V.189, G.190, F.315 Ligands: EDO.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.190 Water bridges: B:V.189 Salt bridges: B:R.173

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

SAM.2: 18 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 Ligands: 76N.29 19 PLIP interactions: 19 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, A:R.309 Water bridges: A:T.188, A:G.190, A:T.248, A:T.248, A:R.309, A:R.310, A:D.314 Salt bridges: A:H.216, A:R.309, A:R.310, A:D.314 pi-Stacking: A:F.294 SAM.33: 12 residues within 4Å: Chain B: G.242, A.244, D.268, L.269, I.292, D.293, F.294, H.295, R.309, R.310, I.311 Ligands: EDO.39 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.311 Hydrogen bonds: B:G.242, B:A.244, 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.3: 3 residues within 4Å: Chain A: R.71, L.74, H.75 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: D.149, E.150, K.178, E.182, R.199 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: E.37, Q.213, S.349, W.350, F.351, P.352 Ligands: EDO.14 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: Y.220, W.224, K.336, V.398 Ligands: EDO.7 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: T.384, G.385, H.387, V.398 Ligands: EDO.6 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: Q.277, R.285, L.289 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: L.156, A.157, R.160 Ligands: EDO.21 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: K.245, W.247, Q.250, G.280, D.281, I.284 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: Y.162, D.163, G.166, I.167 Chain B: G.98 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: K.77, E.80, K.81 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: G.41, K.44, Q.45, W.350 Ligands: EDO.14 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: E.37, V.40, G.41, K.44, W.350 Ligands: EDO.5, EDO.13, GOL.28 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: E.191, S.194, R.195, S.270, G.271 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: R.160, D.163 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: T.128, A.129, R.132 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: A.211, P.215, H.216, T.217 Ligand excluded by PLIP EDO.19: 1 residues within 4Å: Chain A: Y.388 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: R.373, I.383, T.384, G.385 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: A.157, F.180 Ligands: EDO.9 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: G.183, S.184 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: P.197, A.201, M.275, T.278, V.279 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain A: G.136, V.137, N.138 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain B: G.172, R.173, L.174, E.319 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: R.71, L.74, H.75 Ligand excluded by PLIP EDO.36: 7 residues within 4Å: Chain A: V.102, R.106, W.109 Chain B: D.356, K.365, E.366, E.371 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain B: L.289, M.290, A.291 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain B: Y.161, E.169, P.170, T.171, G.172, L.174, H.175 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain B: I.311, D.314, F.315 Ligands: SO4.32, SAM.33 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain B: D.149, E.150, P.153, V.154, K.178, T.181, E.182 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain B: Y.151, K.178, V.189, M.193, M.203, I.362 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain B: T.384, H.387, V.398 Ligands: GOL.45 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain A: T.31, P.33, H.36 Chain B: R.54 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain A: D.48, W.350 Chain B: T.114, R.130 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.25: 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.301, A:H.326 GOL.26: 5 residues within 4Å: Chain A: D.149, E.150, E.198, R.199, N.202 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.71, A:D.149, A:D.149, A:E.150, A:E.150, A:E.198, A:N.202 GOL.27: 8 residues within 4Å: Chain A: D.56, L.57, M.60 Chain B: G.63, T.66, A.67, I.70, W.144 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.56, A:M.60, B:G.63, B:A.67 Water bridges: B:R.130 GOL.28: 9 residues within 4Å: Chain A: E.37, K.44, S.212, Q.213, F.351 Chain B: R.54, D.55, A.58 Ligands: EDO.14 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.37, A:K.44, A:S.212, A:S.212, A:Q.213 Water bridges: B:R.54 GOL.45: 5 residues within 4Å: Chain B: Y.220, W.224, K.336, V.398 Ligands: EDO.42 No protein-ligand interaction detected (PLIP) GOL.46: 4 residues within 4Å: Chain B: S.10, L.11, Q.45, A.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.11, B:Q.45 Water bridges: B:D.12 GOL.47: 4 residues within 4Å: Chain B: E.182, S.184, R.195, H.196 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.182, B:S.184, B:R.195

1 x 76N: 3-[[(1~{S},2~{R},4~{a}~{S},8~{a}~{S})-2-methyl-1,2,4~{a},5,6,7,8,8~{a}-octahydronaphthalen-1-yl]carbonyl]-5-[(1~{S},2~{R},5~{S},6~{S})-2,5-bis(oxidanyl)-7-oxabicyclo[4.1.0]heptan-2-yl]-4-oxidanyl-1~{H}-pyridin-2-one(Non-covalent)

76N.29: 17 residues within 4Å: Chain A: W.143, M.146, G.147, Y.151, V.189, G.190, M.203, M.207, R.310, R.313, D.314, L.355, F.358, L.359, I.362 Chain B: Q.61 Ligands: SAM.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.143, A:W.143, A:M.146, A:Y.151, A:Y.151, A:V.189, A:F.358, A:F.358, A:I.362 Hydrogen bonds: A:R.310, A:R.313, A:D.314 Water bridges: A:G.190, A:G.190, A:S.206, A:R.310

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.30: 5 residues within 4Å: Chain A: W.247, Q.250, A.251, K.254, D.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.254

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.48: 7 residues within 4Å: Chain A: L.140, M.210, A.211, S.212 Chain B: L.52, P.53, R.54 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:M.210, A:A.211, A:S.212, B:R.54, B:R.54 PEG.49: 4 residues within 4Å: Chain B: R.373, G.385, I.386, H.387 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.373, B:I.386, B:H.387

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, J. et al., The crystal structure of FinI in complex with SAM and fischerin. 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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