Structure of PDB 6ydp Chain BC

Receptor sequence

>6ydpBC (length=694) Species: 9606 (Homo sapiens)

VIPNEKIRNIGISAHIDSGKTTLTERVLYYTGRIAKMHEVKGKDGVGAVM
DSMELERQRGITIQSAATYTMWKDVNINIIDTPGHVDFTIEVERALRVLD
GAVLVLCAVGGVQCQTMTVNRQMKRYNVPFLTFINKLDRMGSNPARALQQ
MRSKLNHNAAFMQIPMGLEGNFKGIVDLIEERAIYFDGDFGQIVRYGEIP
AELRAAATDHRQELIECVANSDEQLGEMFLEEKIPSISDLKLAIRRATLK
RSFTPVFLGSALKNKGVQPLLDAVLEYLPNPSEVQNYAILNKKTKILMNS
SRDNSHPFVGLAFKLEVGQLTYVRSYQGELKKGDTIYNTRTRKKVRLQRL
ARMHADMMEDVEEVYAGDICALFGIDCASGDTFTDKANSGLSMESIHVPD
PVISIAMKPSNKNDLEKFSKGIGRFTREDPTFKVYFDTENKETVISGMGE
LHLEIYAQRLEREYGCPCITGKPKVAFRETITAPVPFDFTHKKQSGGAGQ
YGKVIGVLEPLDPEDYTKLEFSDETFGSNIPKQFVPAVEKGFLDACEKGP
LSGHKLSGLRFVLQDGAHHMVDSNEISFIRAGEGALKQALANATLCILEP
IMAVEVVAPNEFQGQVIAGINRRHGVITGQDGVEDYFTLYADVPLNDMFG
YSTELRSCTEGKGEYTMEYSRYQPCLPSTQEDVINKYLEATGQL

3D structure

• PDB: 6ydp Structural insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1.
• Chain: BC
• Resolution: 3.0 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	BC	K541 S543 D613 I624	K493 S495 D565 I576
BS02	rna	BC	I55 D56 R98 H124 R178 K541 R628 E631 K635 Q661 I665 A666 R670 I675 T676 G677 Q678 R704 S705 E708	I16 D17 R59 H85 R139 K493 R580 E583 K587 Q613 I617 A618 R622 I627 T628 G629 Q630 R656 S657 E660
BS03	GNP	BC	D56 G58 K59 T60 T61 I100 T101 P122 N174 K175 D177 S299 L301	D17 G19 K20 T21 T22 I61 T62 P83 N135 K136 D138 S260 L262
BS04	MG	BC	T60 T101	T21 T62

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding

Biological Process

• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0070125 mitochondrial translational elongation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix

External links

• PDB: RCSB:6ydp, PDBe:6ydp, PDBj:6ydp
• PDBsum: 6ydp
• PubMed: 32602580
• UniProt: Q96RP9|EFGM_HUMAN Elongation factor G, mitochondrial (Gene Name=GFM1)