SMTL ID : 5aa5.1

Actinobacterial-type NiFe-hydrogenase from Ralstonia eutropha H16 at 2.85 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-6-6-mer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: V.227, H.228, C.231, R.233, A.234, C.251, I.252, V.253, C.257, G.259, P.279 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.228, A:C.231, A:C.251, A:C.257 SF4.3: 12 residues within 4Å: Chain A: V.227, V.262, C.264, V.266, P.267, C.278, C.285, I.286, G.287, C.288, T.289 Chain C: R.203 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.264, A:C.278, A:C.285, A:C.288 SF4.4: 14 residues within 4Å: Chain A: G.31, C.32, G.34, D.35, G.143, T.144, C.145, I.151, H.152, G.185, C.186, P.187 Chain C: R.79, H.206 8 PLIP interactions: 8 interactions with chain A, Salt bridges: A:D.35, A:D.35, A:D.35 Metal complexes: A:C.32, A:D.35, A:D.35, A:C.145, A:C.186 SF4.7: 12 residues within 4Å: Chain B: V.227, H.228, C.231, R.233, A.234, C.251, I.252, V.253, C.257, G.259, P.260, P.279 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:H.228, B:C.231, B:C.251, B:C.257 SF4.8: 12 residues within 4Å: Chain B: V.227, V.262, C.264, V.266, P.267, C.278, C.285, I.286, G.287, C.288, T.289 Chain G: R.203 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.264, B:C.278, B:C.285, B:C.288 SF4.9: 13 residues within 4Å: Chain B: G.31, C.32, G.34, D.35, G.143, T.144, C.145, H.152, G.185, C.186, P.187 Chain G: R.79, H.206 9 PLIP interactions: 9 interactions with chain B, Salt bridges: B:D.35, B:D.35, B:D.35, B:E.96 Metal complexes: B:C.32, B:D.35, B:D.35, B:C.145, B:C.186 SF4.12: 11 residues within 4Å: Chain D: H.228, C.231, R.233, A.234, C.251, I.252, V.253, C.257, G.259, P.260, P.279 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:H.228, D:C.231, D:C.251, D:C.257 SF4.13: 11 residues within 4Å: Chain D: V.227, V.262, C.264, V.266, C.278, C.285, I.286, G.287, C.288, T.289 Chain E: R.203 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.264, D:C.278, D:C.285, D:C.288 SF4.14: 13 residues within 4Å: Chain D: G.31, C.32, G.34, D.35, G.143, T.144, C.145, H.152, G.185, C.186, P.187 Chain E: R.79, H.206 8 PLIP interactions: 8 interactions with chain D, Salt bridges: D:D.35, D:D.35, D:D.35, D:E.96 Metal complexes: D:C.32, D:D.35, D:C.145, D:C.186 SF4.17: 13 residues within 4Å: Chain F: V.227, H.228, C.231, R.233, A.234, Y.237, C.251, I.252, V.253, C.257, G.259, P.260, P.279 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:H.228, F:C.231, F:C.251, F:C.257 SF4.18: 11 residues within 4Å: Chain F: V.227, V.262, C.264, V.266, C.278, C.285, I.286, G.287, C.288, T.289 Chain K: R.203 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.264, F:C.278, F:C.285, F:C.288 SF4.19: 12 residues within 4Å: Chain F: G.31, C.32, D.35, G.143, T.144, C.145, H.152, G.185, C.186, P.187 Chain K: R.79, H.206 8 PLIP interactions: 8 interactions with chain F, Salt bridges: F:D.35, F:D.35, F:D.35 Metal complexes: F:C.32, F:D.35, F:D.35, F:C.145, F:C.186 SF4.21: 11 residues within 4Å: Chain H: H.228, C.231, R.233, A.234, C.251, I.252, V.253, C.257, G.259, P.260, P.279 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:H.228, H:C.231, H:C.251, H:C.257 SF4.22: 10 residues within 4Å: Chain H: V.227, V.262, C.264, V.266, C.278, C.285, I.286, C.288, T.289 Chain J: R.203 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.264, H:C.278, H:C.285, H:C.288 SF4.23: 13 residues within 4Å: Chain H: G.31, C.32, G.34, D.35, G.143, T.144, C.145, H.152, G.185, C.186, P.187 Chain J: R.79, H.206 7 PLIP interactions: 7 interactions with chain H, Salt bridges: H:D.35, H:D.35, H:D.35 Metal complexes: H:C.32, H:D.35, H:C.145, H:C.186 SF4.27: 11 residues within 4Å: Chain L: H.228, C.231, R.233, A.234, C.251, I.252, V.253, C.257, G.259, P.260, P.279 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:H.228, L:C.231, L:C.251, L:C.257 SF4.28: 12 residues within 4Å: Chain I: R.203 Chain L: V.227, V.262, C.264, V.266, P.267, C.278, C.285, I.286, G.287, C.288, T.289 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.264, L:C.278, L:C.285, L:C.288 SF4.29: 13 residues within 4Å: Chain I: R.79, H.206 Chain L: G.31, C.32, G.34, D.35, T.144, C.145, I.151, H.152, G.185, C.186, P.187 9 PLIP interactions: 9 interactions with chain L, Salt bridges: L:D.35, L:D.35, L:D.35, L:E.96 Metal complexes: L:C.32, L:D.35, L:D.35, L:C.145, L:C.186

6 x MLA: MALONIC ACID(Non-covalent)

MLA.2: 6 residues within 4Å: Chain H: R.325 Chain L: Y.237, P.260, G.306, A.307, S.310 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain L Hydrophobic interactions: H:R.325, L:P.260 Salt bridges: H:R.325 Hydrogen bonds: L:Y.237, L:S.310 MLA.5: 8 residues within 4Å: Chain A: Y.237, P.260, V.261, P.304, G.306, A.307, S.310 Chain F: R.325 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:V.261, F:R.325 Hydrogen bonds: A:Y.237, A:G.306, A:S.310 Salt bridges: F:R.325 MLA.6: 9 residues within 4Å: Chain A: P.267, K.268, G.270, G.274, N.280 Chain F: D.232, P.267, K.268, N.280 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:D.232, F:N.280, A:N.280 Salt bridges: A:K.268 MLA.11: 8 residues within 4Å: Chain B: R.325 Chain D: Y.237, P.260, V.261, P.304, G.306, A.307, S.310 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Salt bridges: B:R.325 Hydrophobic interactions: D:P.260, D:A.307 Hydrogen bonds: D:A.307, D:S.310 MLA.16: 7 residues within 4Å: Chain A: R.325 Chain F: Y.237, P.260, V.261, P.304, G.306, A.307 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:P.260, F:V.261, A:R.325 Salt bridges: A:R.325 MLA.30: 8 residues within 4Å: Chain H: Y.237, P.260, V.261, P.304, G.306, A.307, S.310 Chain L: R.325 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain L Hydrogen bonds: H:Y.237, H:S.310 Salt bridges: L:R.325

6 x NFU: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)(Non-covalent)

NFU.10: 13 residues within 4Å: Chain C: C.81, I.83, C.84, H.88, A.499, V.500, R.501, L.504, P.522, P.523, T.524, C.573, C.576 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:V.500, C:R.501, C:R.501, C:T.524 Metal complexes: C:C.81, C:C.84, C:C.84, C:C.573, C:C.576, C:C.576 NFU.15: 13 residues within 4Å: Chain E: C.81, I.83, C.84, H.88, A.499, V.500, R.501, L.504, P.522, P.523, T.524, C.573, C.576 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:V.500, E:R.501, E:R.501, E:T.524, E:T.524 Metal complexes: E:C.81, E:C.84, E:C.84, E:C.573, E:C.576, E:C.576 NFU.20: 13 residues within 4Å: Chain G: C.81, C.84, N.87, H.88, A.499, V.500, R.501, L.504, P.522, P.523, T.524, C.573, C.576 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:R.501, G:T.524 Metal complexes: G:C.81, G:C.84, G:C.84, G:C.573, G:C.576, G:C.576 NFU.24: 13 residues within 4Å: Chain I: C.81, C.84, N.87, H.88, A.499, V.500, R.501, L.504, P.522, P.523, T.524, C.573, C.576 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:R.501, I:R.501, I:T.524, I:T.524 Metal complexes: I:C.81, I:C.84, I:C.84, I:C.573, I:C.576, I:C.576 NFU.25: 13 residues within 4Å: Chain J: C.81, C.84, N.87, H.88, A.499, V.500, R.501, L.504, P.522, P.523, T.524, C.573, C.576 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:R.501, J:R.501, J:T.524, J:T.524 Metal complexes: J:C.81, J:C.84, J:C.84, J:C.573, J:C.576, J:C.576 NFU.26: 13 residues within 4Å: Chain K: C.81, I.83, C.84, H.88, A.499, V.500, R.501, L.504, P.522, P.523, T.524, C.573, C.576 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:R.501, K:R.501, K:T.524, K:T.524 Metal complexes: K:C.81, K:C.84, K:C.84, K:C.573, K:C.576, K:C.576

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schafer, C. et al., Structure of an Actinobacterial-Type [Nife]-Hydrogenase Reveals Insight Into O2-Tolerant H2 Oxidation. Structure (2016)

Release Date

2016-01-20

Peptides

NIFE-HYDROGENASE SMALL SUBUNIT, HOFK: ABDFHL
NIFE-HYDROGENASE LARGE SUBUNIT, HOFG: CEGIJK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

F
F

H
H

L
M

C
C

E
E

G
G

I
I

J
K

K
L

NIFE-HYDROGENASE SMALL SUBUNIT, HOFK

NIFE-HYDROGENASE LARGE SUBUNIT, HOFG