SMTL ID : 7o25.1

Complex-B bound [FeFe]-hydrogenase maturase HydE from T. maritima (reaction triggered in the crystal)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

monomer

Ligands

1 x CYS: CYSTEINE(Non-covalent)

CYS.1: 14 residues within 4Å: Chain A: I.66, Q.117, R.169, T.278, T.279, A.280, L.315, Y.316 Ligands: FE2.2, CMO.3, CMO.4, CYN.5, SAM.7, 5X8.12 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.279, A:T.279, A:T.279, A:A.280, A:Y.316 Water bridges: A:R.169, A:T.278 Salt bridges: A:R.169

1 x FE2: FE (II) ION(Non-functional Binders)

FE2.2: 5 residues within 4Å: Ligands: CYS.1, CMO.3, CMO.4, CYN.5, 5X8.12 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: CYS.1

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.3: 9 residues within 4Å: Chain A: I.66, Q.117, L.167, M.301 Ligands: CYS.1, FE2.2, CMO.4, CYN.5, 5X8.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.117 CMO.4: 10 residues within 4Å: Chain A: L.167, R.169, G.236, P.276, T.278 Ligands: CYS.1, FE2.2, CMO.3, CYN.5, 5X8.12 No protein-ligand interaction detected (PLIP)

1 x CYN: CYANIDE ION(Non-covalent)

CYN.5: 8 residues within 4Å: Chain A: T.278, T.279, M.301 Ligands: CYS.1, FE2.2, CMO.3, CMO.4, 5X8.12 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: C.1, A:T.279

1 x PYR: PYRUVIC ACID(Non-functional Binders)

PYR.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

SAM.7: 21 residues within 4Å: Chain A: Y.79, C.80, Q.117, S.118, S.146, G.148, L.168, R.169, E.171, R.190, M.209, P.239, F.240, I.241, Y.313, L.315, Y.316 Ligands: CYS.1, MET.8, 5X8.12, SF4.15 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Q.117 Hydrogen bonds: A:S.118, A:E.171, A:I.241, A:I.241 Water bridges: A:G.148, A:E.149, A:R.169, A:R.182, A:R.190, A:R.190, A:R.190 Salt bridges: A:R.190

1 x MET: METHIONINE(Non-covalent)

MET.8: 11 residues within 4Å: Chain A: Q.117, S.118, S.146, G.148, L.168, R.190, Y.313, L.315 Ligands: SAM.7, 5X8.12, SF4.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Q.117 Water bridges: A:E.120, A:S.146, A:G.148, A:R.182, A:R.190, A:R.190 Salt bridges: A:R.190

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain A: V.57, H.62, N.274, N.298, G.349, G.350, K.352 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.57, A:N.274, A:N.274, A:K.352, A:K.352 Water bridges: A:K.352

2 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.10: 6 residues within 4Å: Chain A: E.18, E.21, A.44, K.47, L.48, E.51 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.18, A:E.21, A:A.44, A:K.47 CPS.11: 4 residues within 4Å: Chain A: K.47, I.291, R.294, C.295 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.294 Hydrogen bonds: A:R.294

1 x 5X8: S-adenosyl-L-cysteine(Non-covalent)

5X8.12: 22 residues within 4Å: Chain A: Y.79, C.80, Q.117, R.169, E.171, M.209, P.239, F.240, I.241, T.278, T.279, A.280, L.315, Y.316, K.319 Ligands: CYS.1, FE2.2, CMO.3, CMO.4, CYN.5, SAM.7, MET.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.169, A:E.171, A:I.241, A:I.241, A:T.278, A:T.279, A:A.280, A:Y.316 Water bridges: A:R.190, A:T.278, A:T.278

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.13: 5 residues within 4Å: Chain A: D.347, W.348, G.349, G.350, K.352 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.347, A:W.348, A:W.348 Hydrogen bonds: A:W.348, A:G.350, A:K.352, A:K.352

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

EDO.14: 2 residues within 4Å: Chain A: R.54, R.294 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.54, A:R.54, A:R.294 Water bridges: A:R.54, A:G.341

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.15: 9 residues within 4Å: Chain A: C.73, K.75, C.77, Y.79, C.80, R.83, G.119 Ligands: SAM.7, MET.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.120 Metal complexes: A:C.73, A:C.77, A:C.80, MET.8

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.16: 4 residues within 4Å: Chain A: R.23, K.228, L.269, F.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.269 Salt bridges: A:R.23, A:K.228 PO4.17: 5 residues within 4Å: Chain A: T.279, R.289, P.302, N.303, S.329 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.303 Water bridges: A:T.279, A:R.289, A:R.289, A:R.289, A:N.303, A:N.303 Salt bridges: A:R.289 PO4.18: 3 residues within 4Å: Chain A: Q.314, P.317, G.318 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.314, A:G.318 Water bridges: A:K.319 PO4.19: 2 residues within 4Å: Chain A: T.26, R.27 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.27 Water bridges: A:E.28 Salt bridges: A:R.27

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

CL.20: 4 residues within 4Å: Chain A: R.64, T.113, T.144, R.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rohac, R. et al., Crystal Structure of the [FeFe]-Hydrogenase Maturase HydE Bound to Complex-B. J.Am.Chem.Soc. (2021)

Release Date

2021-05-26

Peptides

[FeFe] hydrogenase maturase subunit HydE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

[FeFe] hydrogenase maturase subunit HydE

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