SMTL ID : 7o1o.1

Complex-B bound [FeFe]-hydrogenase maturase HydE fromT. Maritima (Auxiliary cluster deleted variant)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

1 x CYS: CYSTEINE(Non-covalent)

CYS.1: 16 residues within 4Å: Chain A: I.66, Q.117, L.167, R.169, T.278, T.279, A.280, Y.313, L.315, Y.316, K.319 Ligands: FE2.2, CMO.3, CMO.4, CYN.5, SAH.8 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.279, A:T.279, A:A.280, A:Y.316 Water bridges: A:Q.117, A:R.169, A:R.169, A:K.319 Salt bridges: A:R.169

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

FE2.2: 8 residues within 4Å: Chain A: I.66, Q.117, R.169, T.278 Ligands: CYS.1, CMO.3, CMO.4, CYN.5 3 PLIP interactions: 3 Ligand-Ligand interactions Metal complexes: CYS.1, CMO.3, CMO.4

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

CMO.3: 9 residues within 4Å: Chain A: I.66, V.115, Q.117, L.167, M.301 Ligands: CYS.1, FE2.2, CMO.4, CYN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.117 CMO.4: 9 residues within 4Å: Chain A: L.167, R.169, G.236, P.276, T.278 Ligands: CYS.1, FE2.2, CMO.3, CYN.5 No protein-ligand interaction detected (PLIP)

1 x CYN: CYANIDE ION(Non-covalent)

CYN.5: 9 residues within 4Å: Chain A: I.66, P.276, T.278, T.279, M.301 Ligands: CYS.1, FE2.2, CMO.3, CMO.4 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: 3 residues within 4Å: Chain A: L.78, P.247, L.248 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: D.347, W.348, G.349, G.350, K.352 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.348, A:K.352 Water bridges: A:G.350

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.8: 26 residues within 4Å: Chain A: Y.79, C.80, G.81, Q.117, S.118, G.119, E.120, S.146, L.147, G.148, L.168, R.169, E.171, R.190, M.209, P.239, F.240, I.241, P.242, H.243, A.280, Y.313, L.315, Y.316 Ligands: CYS.1, 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:S.146, A:S.146, A:E.149, A:R.169, A:R.182, A:R.190, A:R.190 Salt bridges: A:R.190

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

PO4.9: 5 residues within 4Å: Chain A: R.23, F.25, 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 PO4.10: 5 residues within 4Å: Chain A: T.279, R.289, P.302, N.303, S.329 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.303 Water bridges: A:R.289, A:R.289, A:N.303, A:N.303 Salt bridges: A:R.289 PO4.11: 4 residues within 4Å: Chain A: F.46, I.291, R.294, C.295 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.294, A:R.294 Salt bridges: A:R.294 PO4.12: 4 residues within 4Å: Chain A: Q.314, P.317, G.318, K.319 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.314, A:G.318 Water bridges: A:K.319, A:K.319, A:K.319 PO4.13: 2 residues within 4Å: Chain A: T.26, R.27 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.27 Water bridges: A:R.27, A:E.28, A:E.28

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

CL.14: 7 residues within 4Å: Chain A: R.64, T.113, V.115, T.144, R.165, M.234, M.301 Ligand excluded by PLIP

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

SF4.15: 11 residues within 4Å: Chain A: C.73, K.75, C.77, Y.79, C.80, L.82, R.83, G.119, E.120, R.182 Ligands: SAH.8 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:E.120 Metal complexes: A:C.73, A:C.77, A:C.80

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