SMTL ID : 7p5h.1

TmHydABC- D2 map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

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

SF4.1: 14 residues within 4Å: Chain A: C.189, C.295, P.296, A.297, P.349, C.350, A.352, K.353, M.480, A.481, C.482, G.485, C.486, G.489 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.295, A:C.350, A:C.482, A:C.486 SF4.2: 15 residues within 4Å: Chain A: V.136, V.152, C.153, Q.157, V.159, V.161, I.162, L.181, C.186, V.187, L.188, C.189, G.190, Q.191, C.192 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.153, A:C.186, A:C.189, A:C.192 SF4.3: 13 residues within 4Å: Chain A: C.143, I.144, L.145, C.146, G.147, D.148, C.149, V.173, C.196, P.197, T.198, A.200, L.201 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.143, A:C.146, A:C.149, A:C.196 SF4.4: 15 residues within 4Å: Chain A: H.92, N.93, R.94, D.95, C.96, C.99, R.101, N.102, C.105, L.107, Q.108, K.142, T.198, G.199 Chain G: T.97 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.92, A:C.96, A:C.99, A:C.105 SF4.6: 14 residues within 4Å: Chain B: V.313, P.331, S.484, C.485, G.486, K.487, C.488, C.491, R.492, S.529, L.530, C.531, L.533, G.534 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.485, B:C.488, B:C.491, B:C.531 SF4.11: 14 residues within 4Å: Chain D: C.189, C.295, P.296, A.297, P.349, C.350, A.352, K.353, M.480, A.481, C.482, G.485, C.486, G.489 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.295, D:C.350, D:C.482, D:C.486 SF4.12: 15 residues within 4Å: Chain D: V.136, V.152, C.153, Q.157, V.159, V.161, I.162, L.181, C.186, V.187, L.188, C.189, G.190, Q.191, C.192 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.153, D:C.186, D:C.189, D:C.192 SF4.13: 13 residues within 4Å: Chain D: C.143, I.144, L.145, C.146, G.147, D.148, C.149, V.173, C.196, P.197, T.198, A.200, L.201 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.143, D:C.146, D:C.149, D:C.196 SF4.14: 15 residues within 4Å: Chain D: H.92, N.93, R.94, D.95, C.96, C.99, R.101, N.102, C.105, L.107, Q.108, K.142, T.198, G.199 Chain J: T.97 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:H.92, D:C.96, D:C.99, D:C.105 SF4.16: 14 residues within 4Å: Chain E: V.313, P.331, S.484, C.485, G.486, K.487, C.488, C.491, R.492, S.529, L.530, C.531, L.533, G.534 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.485, E:C.488, E:C.491, E:C.531 SF4.21: 14 residues within 4Å: Chain G: C.189, C.295, P.296, A.297, P.349, C.350, A.352, K.353, M.480, A.481, C.482, G.485, C.486, G.489 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.295, G:C.350, G:C.482, G:C.486 SF4.22: 15 residues within 4Å: Chain G: V.136, V.152, C.153, Q.157, V.159, V.161, I.162, L.181, C.186, V.187, L.188, C.189, G.190, Q.191, C.192 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.153, G:C.186, G:C.189, G:C.192 SF4.23: 13 residues within 4Å: Chain G: C.143, I.144, L.145, C.146, G.147, D.148, C.149, V.173, C.196, P.197, T.198, A.200, L.201 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.143, G:C.146, G:C.149, G:C.196 SF4.24: 15 residues within 4Å: Chain A: T.97 Chain G: H.92, N.93, R.94, D.95, C.96, C.99, R.101, N.102, C.105, L.107, Q.108, K.142, T.198, G.199 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:H.92, G:C.96, G:C.99, G:C.105 SF4.26: 14 residues within 4Å: Chain H: V.313, P.331, S.484, C.485, G.486, K.487, C.488, C.491, R.492, S.529, L.530, C.531, L.533, G.534 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.485, H:C.488, H:C.491, H:C.531 SF4.31: 14 residues within 4Å: Chain J: C.189, C.295, P.296, A.297, P.349, C.350, A.352, K.353, M.480, A.481, C.482, G.485, C.486, G.489 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.295, J:C.350, J:C.482, J:C.486 SF4.32: 15 residues within 4Å: Chain J: V.136, V.152, C.153, Q.157, V.159, V.161, I.162, L.181, C.186, V.187, L.188, C.189, G.190, Q.191, C.192 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.153, J:C.186, J:C.189, J:C.192 SF4.33: 13 residues within 4Å: Chain J: C.143, I.144, L.145, C.146, G.147, D.148, C.149, V.173, C.196, P.197, T.198, A.200, L.201 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.143, J:C.146, J:C.149, J:C.196 SF4.34: 15 residues within 4Å: Chain D: T.97 Chain J: H.92, N.93, R.94, D.95, C.96, C.99, R.101, N.102, C.105, L.107, Q.108, K.142, T.198, G.199 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:H.92, J:C.96, J:C.99, J:C.105 SF4.36: 14 residues within 4Å: Chain K: V.313, P.331, S.484, C.485, G.486, K.487, C.488, C.491, R.492, S.529, L.530, C.531, L.533, G.534 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.485, K:C.488, K:C.491, K:C.531

12 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.5: 12 residues within 4Å: Chain A: L.20, N.32, C.34, Y.42, G.43, A.44, C.45, R.46, M.47, C.48, T.58, C.60 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.34, A:C.45, A:C.48, A:C.60 FES.8: 10 residues within 4Å: Chain B: C.31, G.33, T.34, C.36, C.78, C.79, G.80, R.81, C.82, L.87 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.31, B:C.36, B:C.78, B:C.82 FES.10: 11 residues within 4Å: Chain B: G.231 Chain C: C.106, G.108, A.110, C.111, C.147, L.148, G.149, A.150, C.151, V.156 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.106, C:C.111, C:C.147, C:C.151 FES.15: 12 residues within 4Å: Chain D: L.20, N.32, C.34, Y.42, G.43, A.44, C.45, R.46, M.47, C.48, T.58, C.60 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.34, D:C.45, D:C.48, D:C.60 FES.18: 10 residues within 4Å: Chain E: C.31, G.33, T.34, C.36, C.78, C.79, G.80, R.81, C.82, L.87 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.31, E:C.36, E:C.78, E:C.82 FES.20: 11 residues within 4Å: Chain E: G.231 Chain F: C.106, G.108, A.110, C.111, C.147, L.148, G.149, A.150, C.151, V.156 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.106, F:C.111, F:C.147, F:C.151 FES.25: 12 residues within 4Å: Chain G: L.20, N.32, C.34, Y.42, G.43, A.44, C.45, R.46, M.47, C.48, T.58, C.60 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.34, G:C.45, G:C.48, G:C.60 FES.28: 10 residues within 4Å: Chain H: C.31, G.33, T.34, C.36, C.78, C.79, G.80, R.81, C.82, L.87 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.31, H:C.36, H:C.78, H:C.82 FES.30: 11 residues within 4Å: Chain H: G.231 Chain I: C.106, G.108, A.110, C.111, C.147, L.148, G.149, A.150, C.151, V.156 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.106, I:C.111, I:C.147, I:C.151 FES.35: 12 residues within 4Å: Chain J: L.20, N.32, C.34, Y.42, G.43, A.44, C.45, R.46, M.47, C.48, T.58, C.60 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.34, J:C.45, J:C.48, J:C.60 FES.38: 10 residues within 4Å: Chain K: C.31, G.33, T.34, C.36, C.78, C.79, G.80, R.81, C.82, L.87 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.31, K:C.36, K:C.78, K:C.82 FES.40: 11 residues within 4Å: Chain K: G.231 Chain L: C.106, G.108, A.110, C.111, C.147, L.148, G.149, A.150, C.151, V.156 4 PLIP interactions: 4 interactions with chain L, Metal complexes: L:C.106, L:C.111, L:C.147, L:C.151

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.7: 22 residues within 4Å: Chain B: G.196, R.197, G.198, G.200, G.201, K.207, N.224, D.226, E.227, G.228, F.312, V.313, G.315, E.316, E.317, K.334, I.350, N.351, N.352, T.355, G.532, L.533 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.312, B:E.316, B:L.533 Hydrogen bonds: B:R.197, B:G.198, B:N.224, B:E.317, B:N.351, B:N.352, B:N.352, B:T.355 Salt bridges: B:K.207 FMN.17: 22 residues within 4Å: Chain E: G.196, R.197, G.198, G.200, G.201, K.207, N.224, D.226, E.227, G.228, F.312, V.313, G.315, E.316, E.317, K.334, I.350, N.351, N.352, T.355, G.532, L.533 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:F.312, E:E.316, E:L.533 Hydrogen bonds: E:R.197, E:G.198, E:N.224, E:E.317, E:E.317, E:N.351, E:N.352, E:N.352, E:T.355 Salt bridges: E:K.207 FMN.27: 22 residues within 4Å: Chain H: G.196, R.197, G.198, G.200, G.201, K.207, N.224, D.226, E.227, G.228, F.312, V.313, G.315, E.316, E.317, K.334, I.350, N.351, N.352, T.355, G.532, L.533 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:F.312, H:E.316, H:L.533 Hydrogen bonds: H:R.197, H:G.198, H:N.224, H:E.317, H:N.351, H:N.352, H:N.352, H:T.355 Salt bridges: H:K.207 FMN.37: 22 residues within 4Å: Chain K: G.196, R.197, G.198, G.200, G.201, K.207, N.224, D.226, E.227, G.228, F.312, V.313, G.315, E.316, E.317, K.334, I.350, N.351, N.352, T.355, G.532, L.533 13 PLIP interactions: 13 interactions with chain K Hydrophobic interactions: K:F.312, K:E.316, K:L.533 Hydrogen bonds: K:R.197, K:G.198, K:N.224, K:E.317, K:E.317, K:N.351, K:N.352, K:N.352, K:T.355 Salt bridges: K:K.207

4 x ZN: ZINC ION(Non-covalent)

ZN.9: 5 residues within 4Å: Chain B: C.468, V.470, H.555, C.560, C.565 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.468, B:H.555, B:C.560, B:C.565 ZN.19: 5 residues within 4Å: Chain E: C.468, V.470, H.555, C.560, C.565 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.468, E:H.555, E:C.560, E:C.565 ZN.29: 5 residues within 4Å: Chain H: C.468, V.470, H.555, C.560, C.565 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.468, H:H.555, H:C.560, H:C.565 ZN.39: 5 residues within 4Å: Chain K: C.468, V.470, H.555, C.560, C.565 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.468, K:H.555, K:C.560, K:C.565

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furlan, C. et al., Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase. Elife (2022)

Release Date

2022-09-14

Peptides

Fe-hydrogenase, subunit alpha: ADGJ
Fe-hydrogenase, subunit beta: BEHK
Fe-hydrogenase, subunit gamma: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
a

J
d

B
B

E
E

H
b

K
e

C
C

F
F

I
c

L
f

Fe-hydrogenase, subunit alpha

Fe-hydrogenase, subunit beta

Fe-hydrogenase, subunit gamma

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