SMTL ID : 3vx3.1

Crystal structure of [NiFe] hydrogenase maturation protein HypB from Thermococcus kodakarensis KOD1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: G.29, G.30, V.31, G.32, K.33, S.34, L.35, N.187, M.188, P.217, F.218, Y.219, L.222, D.223, F.237 Chain B: K.28, S.160, L.162 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.30, A:V.31, A:G.32, A:K.33, A:S.34, A:L.35, A:N.187, A:M.188, A:P.217, A:Y.219, B:S.160 Water bridges: A:S.34, A:S.34, A:D.132, A:L.222, A:D.223 Salt bridges: A:K.33, B:K.28, B:K.28 ADP.5: 20 residues within 4Å: Chain A: K.28, S.160, L.162 Chain B: G.29, G.30, V.31, G.32, K.33, S.34, L.35, N.187, M.188, I.216, P.217, F.218, Y.219, L.222, D.223, V.226, F.237 23 PLIP interactions: 18 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.30, B:V.31, B:G.32, B:K.33, B:S.34, B:L.35, B:N.187, B:M.188, B:P.217, B:Y.219, A:S.160 Water bridges: B:K.28, B:S.34, B:S.34, B:S.34, B:D.57, B:D.57, B:L.222, A:K.28, A:S.160 Salt bridges: B:K.33, A:K.28, A:K.28

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: K.28, G.29 Chain B: K.28, G.29, P.135 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.29, A:G.29 EDO.3: 7 residues within 4Å: Chain A: G.138, D.139 Chain B: R.106, G.107, I.110, D.139, Q.140 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.139, A:D.139, B:G.107, B:Q.140, B:Q.140 EDO.4: 4 residues within 4Å: Chain A: V.65, G.68, G.227, N.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.65 Water bridges: A:L.67, A:V.229 EDO.6: 5 residues within 4Å: Chain B: Y.219, P.220, D.221, L.222, K.225 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.221 Water bridges: B:T.235, B:E.236 EDO.7: 6 residues within 4Å: Chain B: K.175, H.179, K.180, V.181, G.209, V.210 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.179, B:V.181, B:G.209 EDO.8: 5 residues within 4Å: Chain B: Y.97, A.113, E.116, L.117, I.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.97, B:L.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sasaki, D. et al., Identification and Structure of a Novel Archaeal HypB for [NiFe] Hydrogenase Maturation. J.Mol.Biol. (2013)

Release Date

2013-02-27

Peptides

ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog

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