SMTL ID : 3vyr.1

Crystal structure of the HypC-HypD complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-mer

Ligands

7 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 4 residues within 4Å: Chain A: V.17, K.24, R.25, E.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.24, A:R.25, A:E.26 CIT.3: 11 residues within 4Å: Chain A: H.44 Chain B: P.67, V.68, F.98, D.100, P.147, G.148, T.152, Y.358, E.359 Ligands: CIT.5 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.152, A:H.44 Water bridges: B:G.99 Salt bridges: A:H.44 CIT.4: 5 residues within 4Å: Chain B: D.75, A.78, Y.174, R.305, V.310 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.78 Salt bridges: B:R.305 CIT.5: 13 residues within 4Å: Chain A: H.44 Chain B: C.38, T.40, G.65, P.67, G.148, F.149, T.151, T.152, H.202, V.203, E.359 Ligands: CIT.3 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.40, B:F.149, B:T.151, B:T.151, B:T.152, B:E.359 Water bridges: B:H.202, B:V.203 Salt bridges: B:H.202, A:H.44, A:H.44 CIT.6: 4 residues within 4Å: Chain B: L.28, D.29, Y.244, K.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.29 CIT.7: 9 residues within 4Å: Chain A: A.3, P.5, L.52 Chain B: P.4, F.5, R.9, E.229, Y.255, R.257 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:F.228, B:E.229, B:E.229, B:Y.255, B:Y.255, B:R.257 Salt bridges: B:R.9, B:R.257, B:R.257 CIT.8: 4 residues within 4Å: Chain B: R.9, S.10, R.11, E.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.11, B:E.12

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

SF4.2: 11 residues within 4Å: Chain B: C.323, R.324, C.325, C.338, F.341, C.345, V.351, G.352, C.354, M.355, C.362 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.323, B:C.338, B:C.345, B:C.362

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, S. et al., Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation. Structure (2012)

Release Date

2012-11-28

Peptides

Hydrogenase expression/formation protein HypC: A
Hydrogenase expression/formation protein HypD: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hydrogenase expression/formation protein HypC

Hydrogenase expression/formation protein HypD

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