SMTL ID : 6fpi.1

Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.186, H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, P.224, I.243 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.187, A:C.190, A:C.215, A:C.221 SF4.11: 13 residues within 4Å: Chain C: I.186, H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, P.224, I.243 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.187, C:C.190, C:C.215, C:C.221

2 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 14 residues within 4Å: Chain A: I.186, T.226, N.228, C.230, W.235, F.241, P.242, I.243, C.249, L.250, G.251, C.252, A.253 Chain B: K.226 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.230, A:C.249, A:C.252 F3S.12: 13 residues within 4Å: Chain C: I.186, T.226, N.228, C.230, W.235, F.241, P.242, C.249, L.250, G.251, C.252, A.253 Chain D: K.226 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.230, C:C.249, C:C.252

2 x SF3: FE4-S3 CLUSTER(Non-covalent)

SF3.3: 16 residues within 4Å: Chain A: E.16, C.17, T.18, C.19, C.20, E.76, G.113, T.114, C.115, C.120, V.121, G.148, C.149, P.150 Chain B: R.74, H.229 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.76 Metal complexes: A:C.17, A:C.19, A:C.19, A:C.20, A:C.115, A:C.120, A:C.149, SF3.3 SF3.13: 16 residues within 4Å: Chain C: E.16, C.17, T.18, C.19, C.20, E.76, G.113, T.114, C.115, C.120, V.121, G.148, C.149, P.150 Chain D: R.74, H.229 9 PLIP interactions: 8 interactions with chain C, 1 Ligand-Ligand interactions Salt bridges: C:E.76 Metal complexes: C:C.17, C:C.19, C:C.19, C:C.20, C:C.115, C:C.120, C:C.149, SF3.13

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.4: 16 residues within 4Å: Chain A: I.7, V.9, W.11, I.40, L.42, I.72, A.74, S.107, I.110, W.112, I.160, M.163, V.164, D.167, R.168, L.169 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.7, A:I.7, A:V.9, A:V.9, A:W.11, A:I.72, A:I.72, A:I.72, A:I.160, A:M.163, A:V.164 LMT.14: 15 residues within 4Å: Chain C: I.7, V.9, W.11, I.40, L.42, I.72, A.74, I.110, W.112, I.160, M.163, V.164, D.167, R.168, L.169 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.7, C:I.7, C:V.9, C:V.9, C:W.11, C:I.40, C:I.72, C:I.160, C:M.163, C:V.164 Water bridges: C:L.169

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

CL.5: 7 residues within 4Å: Chain A: T.114, W.118, C.120, N.255, G.256, F.257, W.258 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: I.12, H.13, Y.44, D.46, F.95, K.98 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: I.152, P.153, D.154, W.235, N.236, D.237 Ligand excluded by PLIP CL.15: 7 residues within 4Å: Chain C: T.114, W.118, C.120, N.255, G.256, F.257, W.258 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain C: I.12, H.13, Y.44, D.46, F.95, K.98 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain C: I.152, P.153, D.154, W.235, N.236, D.237 Ligand excluded by PLIP

2 x EJ2: NI-FE REDUCED ACTIVE CENTER(Non-covalent)

EJ2.8: 14 residues within 4Å: Chain B: C.76, V.78, C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.509, B:R.509, B:T.532 Metal complexes: B:C.76, B:C.79, B:C.79, B:C.576, B:C.579, B:C.579 EJ2.18: 14 residues within 4Å: Chain D: C.76, V.78, C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.509, D:R.509, D:T.532 Metal complexes: D:C.76, D:C.79, D:C.79, D:C.576, D:C.579, D:C.579

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 5 residues within 4Å: Chain B: E.57, K.399, C.528, V.529, H.582 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.57, B:C.528, B:H.582, H2O.8, H2O.9, H2O.9 MG.19: 5 residues within 4Å: Chain D: E.57, K.399, C.528, V.529, H.582 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.57, D:C.528, D:H.582, H2O.31, H2O.31, H2O.32

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

SO4.10: 5 residues within 4Å: Chain A: R.211 Chain B: G.480, N.481, L.482, A.483 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.480, B:L.482, B:A.483 Salt bridges: A:R.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, R.M. et al., Mechanistic Exploitation of a Self-Repairing, Blocked Proton Transfer Pathway in an O2-Tolerant [NiFe]-Hydrogenase. J. Am. Chem. Soc. (2018)

Release Date

2018-12-19

Peptides

Hydrogenase-1 small chain: AC
Hydrogenase-1 large chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

C
T

B
L

D
M

Hydrogenase-1 small chain

Hydrogenase-1 large chain

Related Entries With Identical Sequence